That's great to hear it's working out for you!
There are only a few (2, maybe 3) ways to launch an external program from the TD environment, and unfortunately they all involve a dang DOS/command prompt window. If I could do away with that I would, believe me.
Let me put a note down on my to-do list to look into adding an option that would bring "focus" (the word you were looking for, I believe) back to the TD application after launching an external program. I need to revisit that code to be sure it will work and be the right thing to do.
In the meantime, what you are doing is fine. The software is written in such a way that you can't launch two instances at a time, and attempting to do so automatically brings the existing one into focus. Additionally, the TD.exe program is really more of a launcher, and it specifically looks for a running instance and, if found, brings it to the foreground and gives it focus. I don't see any drawbacks.