Even if the back window has enough travel to make up for it .. is it going to seal and sit firm, or rattle?
The real issue is that by raising the cap 1/4 inch all your cab bolts are now off-set.
That cab seal is likely to leak decently, even if you have enough play to get those bolts in.
The only proper way to do it would be to mill out a 1/4 inch from the bottom of the cap where your mounting tabs will be, or use full length rails and fill/re-drill the cab bolt holes.
First, no. The window won't rattle. Like I said, it will raise well over a 1/4"more, as I have already measured it. Even if it didn't it's extremely easy to correct it by adding a 1/4" into the channel to put the gaskets where they need to be.
Second, Bolts are easy. Get longer ones for the sides, correct the ones for the front/top. There are several ways to tackle that: Fill existing holes and re-drill near the old ones, add materials as needed, etc. You've mentioned this, already though, and I didn't think it would have had to be mentioned, but since you have, here we are.
Third, you can fix the seals (rear windows) by adding the needed thickness to make up for the difference. Sides are easy, just seal the bottom of the "new" rail cap. The original intent was a full-length rail anyway.
So I don't see any of these things as being a major issue. I could be wrong and may discover so, once I get into it, but the scenarios presented don't seem to be anything that isn't easily overcome That's kind of part of the fabrication process, anyway.
One other way would be to just route out the mounting points on the sides so the cap isn't raised at all, which is an option I am considering. I'm waiting to see how option "A" works, before moving to option "b" in this case.
Lastly, I also have a plan to mount to existing Antenna mounts, instead of under the cap. I like the cap idea better, so working that angle, for now, but may rever to mounting to the Antenna mounts, instead. Dunno yet. Point is, I want it outside of the cab/cap not inside. Inside is just a waste of space and energy, for my purposes.