JohnB I hear you, again I'd be totally fine with doing it all in the background, so long as I can make the vhost conf and OLS setting changes as needed (permanently and without cron patching). Sure dropping in the re-writes via the UI would be nice, and with the way Enhance works actually the probably the preferred options as they rebuild the configs based on internal info. How else will enhance respect my customisations. If it's not done through the UI?
But as a complete hosting system, I think this should be properly considered, its no different than someone installing XX within a website and then getting errors and reporting them to enhance. It will always happen.
For the hosting companies that don't want it, make it optional, for the ones that do, make it known you supply the support. (i.e. maybe the enhance partner program) but cutting off a super useful technology stack due to poor end user behaviour isn't the right way either, it hurts the overall potential of the platform.