Where I'm going with this is, if I have multiple target positions to move to at different ramps, I'd like to do it with a single parameterized move command executed via RUN, rather than 5 move commands in a Stage sequence. Cleaner, easier to trace, insert-best-practice-here, etc.
I love the idea of a single parameterized command executed as a program block, although I wouldn't hesitate to use stages as part of the implementation of that block.
As for your original questions...
Yes, dropping the enable will completely terminate the move.
CTAXCFG largely just initializes values in a structure that are used with the moves. Since the CTRIO/2 register space is limited to a fairly small window, it is necessary to put stuff down in the module ahead of time. Those values can come from profiles, or on the case of CTRIO2, the CTAXCFG instruction. So if you want to change speed and/or accels, you will have to run a CTAXCFG. Can be the same instruction with different values, or a different instruction.
You can change values in the CTAXLIMT and run it as often as you like. We generally made eveything accept a variable that we reasonably could. Most things that will accept a variable will also accept an array reference...so that offers some additional options for abstracting calls.