rM support's statements in the past have been to the effect of "we aren't going to remove the root access; you need it for GPL compliance, and we need it for troubleshooting. And merely using it doesn't void the warranty, but we don't support third-party modifications." So if there's e.g. a flaw in the hardware that you didn't obviously cause by doing something absurd with modifications (e.g. overriding the temperature lockouts, deliberately wearing out the eMMC with writes, ...) they say that it shouldn't really effect your claim.

Now individual experiences with rM support have varied rather wildly between "they're great!" and "they're the worst!" so feel free to temper your expectations.