Ok, as far as I've figured, Steam works this way -- on a 'clean' system, that is one without a previous (or existing) FSX install, it emulates a normal FSX install, so most third party installers wouldn't notice that it isn't a standard FSX, and they'd happily install. However if you have installed FSX before, then it will shift everything enough to make life difficult for addon installers (this would be to make sure that it doesn't interfere with any previous installation), so you'd need to check to see what's installable. As far as general compatibility, though, everything which works in FSX should work in FSX-se, provided you can get it installed.
And as Ian pointed out, a lot of stuff can be dragged over, with a bit of care -- scenery is easy enough, provided you check to see if there are any required files outside the scenery folder, such as elevation 'stubs' in Scenery\World\Scenery.
A lot of developers support FSX-se, so check if there's a new installer. For instance, I've built multi-installers which detect FSX-se for Nelson, the Subscription, and anything released in the future will have a multi-installer.