Of course both supplies are in phase, and in normal operation there is no problem.
The real problem comes when you get a short somewhere on the layout. Then the combined power of both boosters gets to the track. You wlll have a short circuit current of 6 amps instead of 3 amps.
That's the only reason why you should isolate sections.

There may also be a bit of unnecessary power consumption if two boosters are hooked up to the same segment. The boosters may have slightly different delay and they will "fight against eachother" each time the voltage changes direction. If boosters are identical and cabling is reasonably short the problem shouldn't be too big though.

Jack: I had a bad (or incorrectly installed) insulator between two section for some time (I don't know how long). I found it when I was trying to identify all the wires and their destinations. (All right...I know I should have done that when I installed them, but I didn't [:(]). I don't know how long the situation existed but it caused no apparent problems. I am using a mix of IB, 2 LDT boosters, and two 6604's configured as boosters. The short was between an LDT and a 6604. After I found that, I decided to remove all the annoying pickup shoe lifters between segments. I don't like them and I figure if I ran for some time with two segments hardwired together, a momentary connection can't hurt.

Ron,

Thanks for the imput. I have now insulated all sections by the center rail. I have never used the pick up shoe lifters as I don't think they are necessary with digital. The momentary crossing of the booster sections by the shoe should not be a problem unless maybe you got a giant short at that very moment. Even on their big layout at the Toy Fair, Marklin does not use them.

Jack