Finally a post appeared that made me stop lurking and actually sign up to answer, haha.
So, yes, with FX Track switches, all routes are electrically live at all times. This, according to Michael's own writings, is "for our own good," though I personally feel there should be an option to make them work like LEGO 9V switches.
That being said, the intent isn't that you use third-party DCC, but rather that the switches be used as part of the larger FX Track ecosystem which will, eventually, include motors that are designed to be more easily compatible with the PFx Brick, or in the case of the 'smart' motors, will have that functionality integrated. The problem, of course, is that presently there is no way to feed power from the rails through a PFx Brick to a PF or PU motor with off-the-shelf parts. I think this is probably one reason why Michael is prioritizing the power pickup axle over the FX Bricks motors in his product roadmap - to enable the use of a PFx Brick with FX Track and a train motor as early as possible.
In the meantime, with only 'dumb' 9V motors available and the switches not cutting power from diverging routes, we'll have to make do. For my part, I will probably just lift the motor bogie to the side a bit on any train I have parked. Not ideal, but it'll hold me over until the smart FX Bricks motors arrive. Another option would be to insert one length of plastic track near the front of each siding and nudge the motor onto and off of that. Either way, it does mean employing the 'hand of God' but I've observed at many model railroad shows that this is not exactly verboten since all kinds of model railways occasionally need a little persuasion. :P
In the future, there may also be FX Track isolators available, which would provide a means for turning off those diverging routes. But I have yet to hear firm plans from Michael on those, so I wouldn't expect them anytime soon.
For my part, my plan is to upgrade to the smart motors when they're available, which should be sooner than whenever we get isolators.
One other thing: the jumper isolation, as zephyr pointed out, only works for one rail - that's because it's designed for crossovers, in which case when you remove the jumper from each of the two connected switches, then each one isolates one of the two rails from the connected loop so the ultimate effect is isolating both loops from one another. They're not meant to be used for any feature contained within a single loop; you would still get a circuit conflict if you built a return curve, for instance, even with the jumper removed. In cases like that you would need to insert some other kind of isolation, like including a single piece of S1.6 plastic rail, or taping the contact surface between two rails. In the case of a return loop, this would of course mean the polarity would reverse across that gap so a standard 9V motor would get stuck, but a motor controlled by a PFx Brick or some other kind of controller that doesn't care about polarity would be able to handle it just fine.
