As I've mentioned earlier in my post, FBOs are in no way outdated nor deprecated. They were adopted into Core and therefore are considered standard and official.

Perhaps Jason meant to say that pixel transfer and operations are deprecated? While working with OpenGL it is common to accidentally keep using deprecated functionality since in all its mess it is difficult to know what's still current and what's outdated. One way to stay out of trouble is to explicitly request Core 3 functionality, therefore disabling deprecated stuff and forcing you to use only the current features.

The bad news is that Intel IGPs are so popular these days yet they are quite troublesome with OpenGL: while Intel HD 3000 (and HD 4000) supposedly support OpenGL 3, they are quite problematic even with OpenGL 2.1; on the other hand, Intel Atom's IGPs such as GMA 950 and 3150 can barely run OpenGL 1.5 apps with sluggish performance. Therefore, to maintain compatibility, an engine will most likely need to be an hybrid of all OpenGL incarnations.