Yes, it is common practice to tie everything to one common. This is often needed for later on if using TMCC or Legacy, but in general is an expected practice and in many cases of accessories, the way they are expected to be wired and work too.
Phase- not a super hard concept. You have 2 transformers putting out a nominal 18V (technically higher is possible but for discussion we are calling it 18).
With the track and 2 transformers connected on U, if the transformers are in phase, then if a handle is up to 18V on both transformers the difference between the 2 outputs (let's say A post on each transformer is 0 or very near O volts. They are again in phase. If you get this wrong, instead of the 18V nulling out, you get adding voltages- and there is a 18+18=36V!! The reason why that matters is that huge 36V potential could be between 2 tracks where they are isolated at a switch. because a train or your cars (example lighted passenger cars) has 2 pickup rollers- they can bridge across this 2 tracks when crossing such a junction. If the transformers are in phase- nothing happens, there is no voltage difference and the train rolls on through. If the transformers are out of phase, instead of 0V there is now 36V or more. A huge bright spark, massive current, and it may even smoke the wiring or worse.
You phase transformers by adjusting both to a known output (say max throttle or another thing is use a meter and measure and adjust to get say 18V). Then use the meter to measure between the 2 posts- example handle A and handle A both adjusted to the same voltage. The meter between post A to A with U being common connection between the 2 transformers, is either near 0V or near 36 or more Volts. You simple turn the plug of the transformer at the power strip to reverse the phase of one of the transformers.
https://www.youtube.com/watch?v=iASQfnE6pCk
