Has Bob has said it can be difficult to key an upconverted source as clean as a HD one. But however an upconverted background is a different matter, this causes no issue what so ever.

My understanding is that if a signal can be used by the switcher, it is "safe".  Upconverted signals, while not looking as good as natively-created signals, as every bit as valid as any other signal.  As long as the signal is referenced and is locked to the switcher, you should be able to use it any way that you want.  However, keep in mind that ANY upconverter trashes the video to a certain extent...a source that's being "trashed" in any way may not provide as clean of a signal to the chroma keyer (or other keyers) as a true HD source.

Through & Off sources are virtually the same to the switcher; except that Through sources allow ancillary data to be passed (such as captioning and embedded audio).  This ancilllary data (or lack of it) has the potential of screwing up the picture in some cases - I had heard a story about KABC in Los Angeles having problems every time that they took their helicopter shot...turning ON the ancillary data apparently made their framesyncs much happier.  But in terms of keying & using such sources as background or keying material, you shouldn't have any issues.  Just keep in mind that when you pass video through a keyer or DVE, the switcher reclocks it, so you'll use your ancillary data in those cases.  I can't count the number of times that people have asked me why their captioning disappears when they put the network feed into a channel of DVE to squeeze it back, not realizing that when they do this, the switcher strips off & replaces the extra data from the picture.