> Won't this also forbid virus scanners that quarantine files?
Yes. If I really _want_ to execute malware on my device, I should be allowed to do so by disabling the antivirus or disregarding a warning.
> I don't think it's reasonable to expect any manufacturer to uphold a warranty if making unlimited changes to the system is permitted
It is very reasonable and already the rule of law in "sane" jurisdictions, that manufacturer and mandated warranties are not touched by unrelated, reversable modifications to both hard- and software.