No, if you restore the factory OS and the problem persists then in most countries your warrenty is not void. The company has to prove that the custom OS is the issue and if it is no longer installed then it can't be the issue.

> You lose warranty coverage completely, right?

In many jurisdictions, warranties against manufacturing defects (perhaps with a certain limited duration) are mandated by law and non-waivable, and language which purports to disclaim them or have the customer agree to a waiver has no legal effect. To the extent a warranty is discretionary or waivable and properly waived, such an act may void the warranty, but that's not as often the case as simply reading manufacturers disclaimer language would suggest.