Damaged full-suspension linkage surfaces - creaking noises

I am not familiar with this specific bike, but it looks like the intention of the design is this: there's a big oversize bolt on each side, they go through the bearings, and then on the other side between the bearing and that threaded bit in the frame there's a spacer on each side, and the spacer's job is a.) provide a seal for the bearing and b.) connect the inner race of the bearing to the face of the threaded bit such that no metal-to-metal rubbing is occurring.

There's a lot of canned advice in the world to lubricate pivots of suspension frames, but it doesn't actually do anything helpful in many cases. There shouldn't be a metal-to-metal contact at all here. If there still is and the lubrication you've applied is all that's keeping it from being noisy and sticky, no that is not a solution and you will ruin the frame.

If the spacer was somehow out of place or fouled by debris before, and now that's been addressed and it's in place doing its job, yes you are probably good to go unless you've reduced or unleveled the surfaces enough to cause other problems, but you'd probably be able to see that. In other words if everything is tightening down firmly and you can get visual confirmation that there's an air gap and no metal-to-metal rub, that is what you're looking for.

In some cases it can be appropriate to improvise or fabricate hardware to make a suspension frame behave when its stock hardware isn't cutting it. A brand new bike is not usually when you want to be resorting to that, but the climate we're in is forcing such judgment calls. You do want the stock spacers because again (if my understanding is correct) they are acting as seals, but if they're not creating the gap needed then adding some kind of microshim (beer can, sharpie, scissors) might not be the craziest while you're waiting on replacement hardware from Canyon.