Will using the same Steam game library folder on both Windows 7 and Ubuntu 12.04 create conflicts?

I have Steam installed on Win7 in D:\Games\PC\Steam. I installed Steam on my Ubuntu now and for Half-Life 2: Deatmatch it asked wether to install in the default folder or somewhere else. I chose the same folder as for Windows to avoid having games doubled, on Ubuntu it's /media/Media/Games/PC/Steam. It didn't download anything and was instantly ready to play. When I chose to install Team Fortress 2 it didn't ask me where to install. I read that some games, like TF2, can be installed only in the default game library folder. Will those that are installed in the same folder as the Windows Steam is create any conflicts?

Thanks in advance.