I think it's always pretty useful to look at things from the perspective of 'what do the writers seem to want out of this', and I think the 6.4 development really helps in making me pretty confident about that.
I think they're essentially setting up shard travel to sit comfortably in the 'maybe later' pile. Y'shtola's reached the point where, essentially, the theory is sound but we're just not in the state where it can be put into practice; the circumstances that allow for voidgates between the Source and Thirteenth just aren't present between other shards, even if we're now closer to understanding why they're happening in the first place.
I think that tracks for what the writers may want to do with this, because it serves two purposes:
1. Gives Y'shtola a long-term potential goal and arc; she's always sort of lacked that, and this would do a good job at solving it, even/especially if it takes her out of the 'Core Crew' for a while.
2. Lets the notion of exploring other shards sit as a long-term possibility, but not one that's going to happen immediately; essentially, to put it out of mind while we focus on going to the New World, or Meracydia or whatever. A hook for future expansions, but not the IMMEDIATE future expansion.
It also, as a side benefit, clears the path so that the OP's concern is DEFINTIELY alleviated; no, Y'shtola and the MSQ Crew aren't going to interfere with CB&U, they can do their own things without mandating crossover in the process.