I do a lot of 4th axis work, and work with the spin indexer and as you say getting close to it can be problematic. Here are a few workarounds I have come up with. I have a Tormach 1100 with 18" of "Z" and still try and manage tool length.
As mentioned getting close to a 3 jaw or indexer is tough using ordinary drill chucks or end mill holders, most of my work uses 1/4" or smaller end mills and drills. My CNC Tormach uses the "Tormach Tooling System" which is pretty much everything is in a 3/4" collet. All toolholders have a flange that buts against the spindle nose which gives you repeatable tool height. set the tool height once and enter it in the tool table and you can take it out and put it back and "Z" zero won't change. If you switch tools just enter the tool number and it sets the "Z" zero.
These are my ER11 collet holders, they have a 3/4" shank. I made a bunch of collars to use as the "Flange" machined a snap ring groove in the shank and they are all qualified. I can get right up next to the indexer and my 4th axis with these.
On the right are some of the flanges with snap rings. And just below them is a piece of 3/4" drill rod with a snap ring groove machined and a knurled spot to hold the flange. I use these blanks for what ever I need a special tool holder for Or a tool I use so much I don't want to waste a drill chuck for. On the bottom left about 7:00 you can see one i used for an 1/8" spotting drill.
And here are a bunch of other common drills I use a lot, Tap and clearance drills. All set up in the tool table.
I don't know if I have mentioned it before but I am a tool junkie
Here is the rest of that drawer above. All of these tools are in the Tool table with the "Z" height and diameter defined just enter the Tool Number and go.
I apologize for going a bit off topic.
Scott