answers may be found in the stars...

a notable example of paints that generally are meant to combine with each other is all of the creepy & cute paints. the paint themes even combine all of these together

anyway, all of these vanilla paints align with each other! theyre all also called stripesLL

and on a similar note, stripesML

but something like the amigurumi paints isnt what im talking about. theyre all named the same, and go togethre nicely, but i mean specifically the patterns, as in the above stripes paints

anyway the cow spots coat and detail paints combine, and one of the paint themes also takes advantage of this

the halftone and halftoneUnderside dots align with each other sometimes..?

the lateral paints align, though the detail one completely overpowers the coat one. im not sure thered be much application to this

the polkadot paints work in a very similar way to the cow paints! one of the cell paints also basically does this exact thing, except with one base paint (cell paints are base paints that look like paint themes isnt that fun)

ridgesLateral, kind of a better version of this with the lateral paints

for the creepy & cute paints, there are still some particularly notable examples of paints that have aligning patterns:

feltStitch base and coat paints

toonCritter base and detail paints (the detail paint borders the light stripe on the back sort of)

dottie base and coat paints

Frankenstein coat and detail paints (the base paint also sometimes aligns, but the stitches dont seem to be designed to align)

as you can see, all of these alignments are totally intentional, and tend to be between paints that all share the same (besides parts of the name like ce_skinpaint_base_[something]) internal names