Well, it's frames vs fields, so yes, there can be a difference. Transcoding from progressive to interlace is usually not an issue. Transcoding from interlace to progressive can introduce transcode artifacts.
As long as your original media is progressive, the Project is progressive, you should have no quality issues.
To the matter at hand, the project in FCPX and the project in DVD Architect must both be DF or NDF. Mixing the two does in fact mess up timing for things like markers. DF loses roughly a quarter frame or so each second, to the same video in NDF. We run into this all the time with The Louisiana Film Channel when filmmakers don't follow submission specs.