Order the right flex plate (with slight modifications to the torque converter bolt holes) and spacer and it bolts up the same way as the 4l60e. The bowtie overdrive kit is not hard to install at all. Follow the instructions for the setup and it works just fine.
It isn't that much more work. The question really comes down to what you are using on the engine side of things. Throttle type? Going 700 will require a cable throttle. The 60 will take either. If you plan on going drive by wire, you have to go with the 4L60e. Next is harness and PCM type. Running the stock 5.3 harness you should be able to go with the 60 without too much issue. I'm certain there are a few changes between the 94 4l60e and the later versions running so you need search out if there are any wiring differences between the years. You could run an aftermarket controller for just the trans and remedy any differences to the stock 5.3 harness and earlier 4l60e. Obviously, the 700 don't need the PCM to work, so it really don't matter what you used for the engine.
There are pros and cons for each. It really depends on those factors and your budget. In my case the budget is always skinny. I already had the 700 in the truck. Since my 5.3 didn't come to me with a flex plate already, I had to buy one. The part number I used was for a 4l60e anyway, just a quick trim with a die grinder to oval out 3 holes. No added cost over going 4l60e. I had a cable throttle to start with. Only extra cost I had was to run the bowtie overdrives tv cable kit. That by itself was cheaper that finding a 4l60e. Plus in my case since I'm using an aftermarket controller and harness that does not have provisions for the trans I would have had extra expense in getting a stand alone trans controller and harness.
Don't get me wrong had I had the budget for it, a new 60e and TCI controller and harness would have been the ideal way to run for me.