Greetings, firstly let me say - amazing mod pack, I love it :)
I'm popping this under ideas/suggestions as this absolutely is not a bug.
In using pymods, they generally play together really well with Kingarthurs compatibility patch. Aside from duplicates which are no issue at all, I've found one issue that required me to change a value in your library:
When you override the boiler the temperature for steam is set to 120, I've changed in manually to 165 since I've found two receipes in py that require 165 (and I can't find another way to get exactly that temp).
As I say this is not a bug; tbh I rarely report/highlight things, I just fix/edit them myself, but I thought I would for this one, if only as info for other players - as without this change it may be rather opaque as to why two particular py receipes don't work.
For reference to other players wanting to make this edit:
In Phasma's library mod: got to C:\Users*YOURNAME*\AppData\Roaming\Factorio\mods\apm_lib_0.17.78.zip\apm_lib_0.17.78\lib\utils
(or wherever else you might have your mod files).
Now got to the 'boiler' file and change the value on line 66 to '165' - your claypit and raw fiber recipees will now work :) Note there are two other work arounds I can think of, but this one is quickest (maybe dirtiest) to do lol
One side-note, I can't find anything specifically that requires 120 steam temp at my stage of the game. If in the early game 120 is required, a player could leave the value at 120 and then when they get to the stage of needing py's stuff, like clay, they can change the value to 165 (as you shouldn't really be needing, or be reliant on anyway, phasma's stuff at this point).
I hope this idea helps. But even if not - love, love, love your modpack, sooo many pipes, I dream about them ><