Space Exploration removes space-science-pack, however it scans all recipes in postprocess to replace it with its replacement, however that doesn't seem to happen with this mod for some unknown reason (perhaps ordering?). Detecting SE and using its sciences as appropriate directly would fix the issue. :-)

My recipes and technologies are all defined in data.lua phase, which is the first data phase. Other mods should be able to modify my prototypes in any data phases.

I do not play SE, so I have zero knowledge of whatever new science packs they are providing.
Maybe some players who have both mods will know the relations of between science packs of the two, but that would not be me.

Interesting, thanks, must be an SE bug, reporting it there as something isn't changing then...

Essentially the vanilla science pack is removed, in it's place is a set of packs starting with a Rocket Science Pack or something like that (then splitting to material/space/energy/andsomethingelse), then goes to deep space science for endgame science.

Wish you luck on SE side then.

BTW, such support will never be "built-in" into my mods. I consider this mod as "medium"-sized, while not as big as the popular overhaul mods, my mod still has non-trivial number of new tech and recipes. There are too much changes to handpick, especially for whom have no knowledge of those modded science packs and resources.
This is when the so-called "bridge mods" come into play. You can see a lot of such for the overhaul mods (Angel-Bob, Krastorio, K2, pY, Seablock, ....). Most of them are managed by players who know both sides well enough, knowing how to balance and adpat.
And the best part is let the players choose which bridge to go, in case multiple mods try to modify the same tech/recipe. I think it is not uncommon that players are using multiple overhaul mods at the same time, right?

Do you have a recipe that uses the science pack as an ingredient or something?

The space science removal code goes through technologies, but I don't think it removes it as an ingredient from recipes.

That's precisely it, the higher level tanks take space science packs 'as' an ingredient, so since SE removes it then it should fix up recipes as well.

I think this is the first mod I've seen that uses them as crafting ingredients, no wonder it got overlooked...

Yeah, I don't think I'd seen it before either other than via recipes generated based on its existence.

Ah, alright... OP mentioned

Space Exploration removes space-science-pack, however it scans all recipes in postprocess to replace it with its replacement, however that doesn't seem to happen with this mod for some unknown reason (perhaps ordering?)...

Yet Mernom seems to say only technologies (not recipes) got replaced. So which is the case?
And more importantly, has SE solved it now?

The appearance of science pack in crafting item recipes is an abstract representation of science and engineering effort required into those high-end tanks. They are never mass-produced, but probably very limited in numbers. The production process of each prototype requires tremendous engineering work. So I have used military science pack (in super-heavy tanks) and space science pack (in MK3 tanks), to represent the extra engineering work required to assemble these hi-tech beasts into one working piece.
Also, unlike overhaul mods, I do not have tons of advanced resource types or materials as ingredients in the late- or post-game. So space science pack is among the best items to be used as ingredients here. ;-)

And more importantly, has SE solved it now?

Looking over its changelog for the SE-postprocess mod I don't see any such bug fix mentioned, so I'll lean to no so far.

Right now to work around it I keep the new Satellite option in this mod disabled and have SE add the space science back but via a recipe (once you've launched off planet) renamed as Optimization science pack.

The appearance of science pack in crafting item recipes is an abstract representation of science and engineering effort required into those high-end tanks. They are never mass-produced, but probably very limited in numbers. The production process of each prototype requires tremendous engineering work. So I have used military science pack (in super-heavy tanks) and space science pack (in MK3 tanks), to represent the extra engineering work required to assemble these hi-tech beasts into one working piece.

Rocket Science is the lowest tier science that must be done in space in SE (in addition to almost 2 dozen more that can only be done in space), replacing it with one of those is definitely of an "end-Nauvis" feel, as by that point you are getting pretty close to wiping out a planet of bugs anyway (well, a dozen or so more research packs in then you can literally do that), so rocket science for end-tier tanks/spiders makes sense as by that point you're in space and the bugs are starting to look small at that point anyway, even on death worlds, but it's not so late that the bugs are a non-issue yet. Though keeping the sciences terrestrial (pre rocket/space) could also make sense as it is a terrestrial problem that it's helping solve. Perhaps an option?

Also, unlike overhaul mods, I do not have tons of advanced resource types or materials as ingredients in the late- or post-game. So space science pack is among the best items to be used as ingredients here. ;-)

If rocket science is detected then replacing it with rocket science packs would be very end-nauvis (as that has to be built and researched in space itself, so you need a pretty decent logistics system setup to be getting resources up there, it's definitely "after" space science in vanilla factorio). As for end-game resources, SE does not add anything early-game (short of like glass and sand and such), but late game there are a multitude of resources that can only be acquired off-nauvis, whether in an asteroid belt or on other planets, and I think it was holmium is considered the 'super strong' material (short of naquada, but that's very end-game even for SE and by that point you can eradicate bugs off planets in a couple of different ways) and it's about a quarter of the way between rocket science and naquada or whatever it was called, so it's not "too" late but is considered a very very strong material if you wanted to add it as a necessary ingredient, though by that point the bugs are starting to become less of an issue, I guess it depends on where you'd want it all to fit in the tech tree between end-nauvis and being an interplanetary force that can wipe entire planets out?

EDIT: For note, the Optimization Science Pack in SE only exists when enabled in its options, it quite literally is the vanilla space science pack except it can only be acquired via recipe that uses some off-world materials, so it's a good bit past end-nauvis, but it only exists for the purpose of inter-mod compatibility like this so it lays on the latter part of the tech tree for balance/safety, which may not really fit with what is expected for space science. It has no role in SE and hence is disabled by default. The options for it are disabled, replace space science with rocket science, or optimization science pack (with two optional recipes, both well long past end-nauvis), sadly the replace space science with rocket science option only works on technologies, not on recipes...