I'll go with the following:

Clips in, doesn't connect to power, can be unclipped and leave no trace: No change to warranty. If it came in for repairs, the mod might be removed to get at something to repair, and placed in the cash box for the customer to reattach on their own. Exceptions would be made for things like replacement bumper caps and acorn nuts.

Clips in, ties into GI: Depends on the item and how "marginal" the power ratings are in the game as "stock". If the mod takes advantage of a socket, and can be proven to have less draw than the piece it replaces. Likely would be removed for repair, customer would need to reattach it.

Requires mount added (i.e. drill holes somewhere): Unhappy noise will be made. If it also ties into GI, will void warranty because of the mount requirements. Depending on the mounting method, it might void the warranty even without tying into the GI. Would be removed for repair as best as can, returned to customer to reattach on their own. (You should sense a theme here.)

Replaces electronic function more significant than lighting: Would void warranty. If brought in for repair, mod would be removed, returned to customer to reattach. If mod was responsible for fault, customer would be informed of such, note would be made to add extra surcharge if comes in again for same fault with same mod. Note: it is up to the customer to learn to not to reattach the mod if they lather, rinse, repeat with the mod.

Basically, if it's entirely cosmetic, isn't something that can do damage, and can be removed with no trace, I'd let them keep warranty. If it involves modification or a substantial replacement of part of the machine that isn't just cosmetic, then it's likely the warranty would be voided.