In choosing an FTDI breakout board, in easy/beginner's terms, what is main difference and advantage/disadvantage of having DTR vs RTS brought out to pin 6? Should I commit to one vs the other? Would it be useful and/or practical to modify a board (like using a mini-switch or header/shunt combo) so that I have the ease and flexibility of being able to switch and choose between the two? Or, do I need to make a more fixed modification like cutting the default trace and using a jumper wire? I just don't know enough to make a decision on which way to go. I don't mind putting in the extra time up-front to do a modification that will give me useful flexibility.

If you are using a Mac or PC then the DTR is the one that is toggled when ever the serial port gets assigned / un assigned. In some flavors of Linux this is done with the RTS line.
That’s all.