The GameTooltip Frame is currently the only part of the interface that always has 100% alpha (aside from chat, which has options).
Turning off UberTooltips is the only real way to make them any less obtrusive and even that requires Advanced Interface Options.

Fading Tooltips during combat or even just making them blend in slightly more would be a nice feature.

I know some other Addons currently have major problems with that one, so it might be hard to actually implement,
thought that might stem from those Addons' main purpose of moving around parts of the Interface being mostly baseline.

I don't think i want to wrap my head around the GameTooltip for now. Since it has a lot of actions updating it, I would have to try and hook all of the for fading purposes. And i think it likely for taint as well.