The main value in assembly level cuts is when the part will be cut differently depending on where it is installed - and it does a fine job of simulating match machining. The price that's paid for it, as others have mentioned, is that it is building a hidden family table of each part being cut (so you don't have to) and managing all the variant models (which makes it seem slow).
The problems I've seen people have explicitly is making poor reference choices. One that I recall offhand is someone who used the part surface that was being removed as a reference. The first time the assembly regens, it was all good, but the next regen sees the surface has been removed and the reference with it - causing a failure.
Also, as mentioned already, is the need to prevent auto-select from selecting items you didn't intend to get cut. I don't know how smart PTC is about this but it's possible they would generate a hidden family table for items that don't actually intersect. This also means errors about failing to intersect with the assembly cuts.
For this particular case, I find building a casting model and then creating a separate part using the casting as an inheritance feature works fine. It gives a chance to create alternative machined versions from the same casting without tying the resulting machined versions together. If they needed to be tied together, they could have a family table in the machined part model.
Giving the finished part drawing to the casting people is a good way to get draft where it isn't wanted resulting in interferences where it is unexpected. The alternative is to provide complete coverage in terms of tolerances, which is also workable, but often as much work as laying out a precise shape, and is more likely to cause problems moving the part to a different supplier who will also start from scratch figuring out what they need to do to cast the part correctly.
Aside from that, I can't fault other options for the conditions people operate under. Each place has it's own environment and each has its own best solution.
