You won't find too many bugs in vanilla quake with FTE, since I tried to report them all and Spike did fix a lot of them. There were some game breakers in the mission packs IIRC and those should be fixed now. You will find more issues in Quake 2 for instance, and I have never tried Quake 3 with FTE.
On the flip side, I tried to do a lot of things in my game that really took the engine to the edge of what it could do. I used most of its non-Quake features. All these things should have been doable, but if you break new ground then you are likely to run into bugs that simply no one else encountered before. Spike does fix bugs. but in the end there was a list of two dozen bugs or so and they just lingered. Some were highly visible, such as fullbright models if a patch mesh used the same texture, or solid world outside heightmap terrain. Bugs like the latter actually break the game. Please note it's entirely possible that they are fixed now.
On the whole I would be unwilling to depend on any of these engines for a commercial game, unless I had a really good programmer on my team who can fix bugs (I can program, but I am not an extended Quake engine specialist and I really don't have the capacity to become one.) I am under the impression that both DP and FTE are hobbyist projects and if you run into a lot of bugs after release, you might be caught between an angry crowd and an engine you can't fix yourself. This is one good reason to not use them unless you are sure you can cope with a post-release engine bug tracker. Basically all risks are yours and yours alone.
With Unity, you can at least point at them when something happens and you can be sure that the engine is tested by a shit ton of people, so it will be more stable no matter what. It's just reasonable to use the stable and well tested, well documented alternative with the huge community.
motorsep: OK, but if you make (3D) indie games, especially in modern engines, I would expect that you eventually have to learn a 3D modelling suite anyway or have someone on hand who can. You won't get far without it

And yeah, it's not that easy to decide between Unity and UE4. I think in the end, you can make a game with both. Question of taste.