Maraxsis adds a Research vessel tech for compacting science packs for rocket launches with recipes to pack and unpack. Cubium adds Cube Mastery 4, which adds slight variations on regular science pack recipes but with added materials for greater output. Both of these technologies add many different science pack recipes, but they aren't intended to be the way to obtain said science packs in progression. Indirect dependencies on yellow and purple science for Cubium, and those plus the vanilla inner planet science packs for Maraxsis's Research vessel help out this mod to narrow down the actual science pack techs, but for the science packs from modded planets that get recipes from these, Science pack dependencies just has to trust that they already exist as indirect dependencies, which in the case of Secretas & Frozeta, they don't. (Secretas & Frozeta was the primary reason I added this mod.)

Unfortunately, I don't know of how to make this generic without either a heuristic that a given tech should only give one science pack, or an explicit blacklist with maraxsis-research-vessel and cube-mastery-4.

P.S. Igrys also adds many science pack recipes, but they seem to be invisible to Science pack dependencies, so they shouldn't need special treatment as well.

The science packs causing issues with maraxsis-research-vessel and cube-mastery-4 are those that don't get unlocked before them. There are then multiple candidate recipes, with none being strictly earlier then the others. So I don't have an obvious recipe to pick. The quick fix might be a setting to allow blacklisting those technologies. Proper analysis on what becomes craftable when would be better, but that's a can of worms as I then have to properly figure out when any kind of resource source becomes available, and it still wouldn't resolve cube-mastery-4 since you could e.g. discover Secretas & Frozeta, get gold there and then use the cubium recipe for the science pack, never researching the proper golden science pack recipe. You'd have to ship some cubes to Frozeta, but since it appears that you can have multiple that might actually be a reasonable thing to do, even if it may not be "the intended way".
Sadly technology dependencies don't support an "either or", maybe I can insert a fake trigger tech with some scripting that auto-unlocks once either dependency is met. That still messes with the ability to queue researches across that tech, but shouldn't prevent any weird but possible ways of progressing. I'll have to think about that.

Regarding Igrys: Looks like all of it's "enhanced" recipes are created with enabled = false without a technology to unlock them. Since those recipes will never become available, they get ignored. There's a hidden setting that forces enabled = true, but then these recipes will all be available at game start which causes Science pack dependencies to do nothing as there are no additional dependencies needed.

Just uploaded a new version. The blacklist you suggested can now be found in the mods settings. I've also played around and implemented approach using. Please let me know what you think about it.