I guess I need to spend more time reading these posts before I post back. Let me try to clean this up, You love the tapeless camera, and you want to just archive quicktime files in the least amount of time. And you figured out how to joint spanned clips but it takes too long.
First off the EX tapeless workflow is no different than the DVC Pro P2 workflow, and most people preserve or archive the original files created by both systems as you should consider. The original EX files can be converted to PC or Apple formats very quickly and you may have a client that needs to use the files for something other than Final Cut at a later date.
Then you asked about reducing the time it takes to download both or at least one of the cards to joint spanned clips. Well, you must pay the piper for not having to tell your client you need to stop and change a tape as you crossed the recording of the clip to the next card. Joining a spanned clip takes what it takes to mate them up, but you didn't lose the shot as with tape you would have stopped at an hour. You could conceivably never stop rolling with a tapeless system.
I think you may have said you will try an avoid cross card clips. My point to try and reduce your download time was meant for non spanned card clips as I understand time is money. Sorry if I confused you.
I honestly don't think of dragging and dropping files is as much work as capturing, it requires no supervision like capturing, however it does take some time and if you are sitting there waiting just for this to happen then it may take more time than capturing to first copy the original files then re-wrap them into quicktime files to edit with, not to mention coping these original files to a second drive for backup or worse yet burning these files to SD DVD's. Your 20 years of tape workflow may take some time to adjust to this tapeless file managing world we now live in.
Beyond all that you asked about Sony has licensed the EX codec to JVC and they may have what you are looking for, they are using the Mpeg-2 (HQ 35Mbps) codec but they are wrapping the original file to quicktime .mov (as an option) from the start while using SDHC media, so you may consider the MxR/SDHC as unapproved but it is really out there and working well for many EX users. Here is your tape equivalent = MxR/SDHC
Another solution for you to reduce time and get original quicktime files would be to invest into the Convergent Design Flash XDR (or the Nano Flash that is coming soon). This is a HD-SDI recorder that allows you to choose the compression you desire that goes way beyond the limits of the camera manufactures, which allows you to take full advantage of the amazing cmos exmor sensors in your ex camera choosing compression levels from blueray to HDV to EX Cam HD 50Mbbps 4:2:2 to 100Mbps all i-frame with near uncompressed quality, using 32 gig CF cards that are under $80 a piece.
FYI There aren't to many people on this forum that care to help XD cam users with questions that are really specific to Sony's EX workflow system so you may want to check out the Creative Cow or DV Info if Final Cut isn't a part of the question. I hope I helped you find a solution to your question and I was at least helpful.
Z1