Basically, I'd say take a deep breath and relax.
You've caught a problem before it has become a problem. The stain around the boot is most likely dust or rust stains. As long as the crack does not penetrate all the way through, you're ok. Flex Seal after a thorough cleaning will probably be a long-lived stopgap.
The axles are designed to be replaced without loss of transmission fluid. The transmission seals for the output shafts are inboard of the axle and the axle mount itself.
Take a look at the following video from about 6:25 or so. When the axle pops free at ~7:20, you'll see there's absolutely no outflow of transmission fluid:
If the CV boot fails, under most circumstances, you have many miles before the joint even gets noisy, and it can be noisy for a very long time before it breaks.
Split (not slip) boots have been available since the days when axle boots first were put on cars. However, the most commonly available ones are from Dorman, a supplier with a very spotty record. It's possible that the negative comments about split boots are more directed at the terrible quality of many Dorman products than at the design of the boot itself.
That said, when the time comes, it's best to pull the axle and replace the boot with a non-split boot. And, as you say, at that point, it's probably best to simply replace the axle, since they are relatively inexpensive.