Sure it's an issue. Just for example, when I exit out of TOTD:OK an ad pops up from the steam engine. I don't want that crap on my arcade cab. Even if I didn't mind it wouldn't matter because that game requires an online connection.
So long as it's a physical disc, the game can be cracked to omit needing the disc. With steam the games can be cracked for sure, but generally the "crack" is running a fake version of steam, which will give you the exact same issues depending upon the game.
Under Steam>Settings>Interface, uncheck "notify me about....."
That said, I still haven't worked out all the issues to seamlessly incorporate it into a front-end.
It was working well when automatically signing in, except for when there was an update or I had signed in on another computer.
Using the command lines to automatically log in resulted in it taking focus away from my front-end.
In offline mode, I get a popup when the game is launched asking if I'm sure that I want to launch it in offline mode.
I'll crack it eventually, probably with autohotkey, but it is far from front-end friendly.
For now, I've just resolved to signing into steam before launching the front-end if I intend to play any steam games.