For the GUI, I know for sure that at least ChessGUI and Arena support the time controls in seconds, winboard probably too. It should be ok with the winboard engines : I think time is sent in seconds or milliseconds, and I imagine that almost all of them try to spend all the time remaining in the last moves before TC. But maybe that new bugs would unfold then ... And would the emphasis on time be quite different is hard to tell and might vary for every engine, although I am quite confident it shouldn't twist results in a significant way.
However you're certainly right to test in fixed conditions and to stick to your parameters. The best advantage of a rating list is its solidity and its durabilty. It reflects what happens under certain conditions and changing them even slightly to take care of bugs of engines is not worth it.
I see you have announced many engines with the"horrible bug" in the thread, it could be nice to have them all in a list.
Best wishes and thanks for all the testing results and statistics that we are many to read.