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I understand that this is both a modelling/painting and background question, but i'm because i'm looking more for precedents, i'm going to post here first.

Basically, i'm in the process of creating what i have dubbed Mark 5a Power armour that my Space Marine characters are going to be wearing (yes, its a parody). Basically, imagine your generic mark five suit, except, no studs. Or in simpler terms, rimless studless pauldrons, studless greaves and knees, no external cabling on thighs, but with the signature criss-cross cable on torso with the circular grill in the centre (i need it for visual purposes so the players know what the origin story is).

These firstborn Marines wear red power armour, with white shoulder pads (although i can't decide between having them of a Blood Angels lineage or Raven Guard)

So on the left pauldron, i have the Chapter Insignia, but on the right pauldron, im going to have a simple numerical designation, IV in black font. Now my question is, since the numeral on the right pauldron (in this case, the IV in black font) usually indicates squad designation, is there a precedent for the colouring of the lettering be a stand-in for the company designation (so if the IV is in black, would that mean i've designated the marine as belonging to the 4th Squad of the 5th Company)? Or will I have to resort to painting a knee in a different colour to represent a company.

You're already breaking the codex standard so you can just make up whatever you want

I've flicked through Insignium Astartes and couldn't see any examples with you specific method of marking company.

That said, the methods listed include company colour on pad trims, chest eagle, kneepad (left or right, usually left), and helmet stripe, with company numeral on kneepad also being common. One had colour and numeral on the left greave.

Several dont display company markings at all.

In short, your scheme fits fine within the broader variety of methods.

I agree with the above. There's precedent for variation, and having the color of the squad number denote company isn't far off from the codex-standard of trim color doing the same.