I agree, and certainly one of the obstacles to making this kind of archive is separating the organ's tone from the room's contribution. And, as you say, the organ and the room ideally become "one" when an installation is properly done. The electrical signal coming out of the tone generator is just "raw material" for the real "organ builder" -- the installer/voicer.
Perhaps one do-able project would be to collect a set of recordings from the line-out jacks, as you mention, of a variety of organs of different builders and of different eras. For example, from Allen one could get samples from an analog, a MOS, a MOS-2, an ADC, an MDS with full cage, an MDS W-5, and a Renaissance. From Rodgers, an analog, a PDI, a PDI-2, a Trillium, a Masterpiece, an Infinity, along with maybe some of the second-tier models such as the Cheetah, the Allegiant, and so on. Then, if possible, add to the collection some Viscount, Johannus, and Baldwin samples.
So, this might add up to 20 or 25 organs being "sampled" in this way. Even that sounds like a daunting task! Something that would keep me occupied for a good while if and when I can mange to "retire."
But, this collection of dry, right-from-the-jack organ tones would not necessarily be very pretty. It would be simply an academic exercise in order to show how much alike or different the various dry tones are on the same stops or choruses.
An alternative project would be to collect recordings of actual installations done by the various builders over the decades. But of course such recordings are already available to some extent. Most companies have issued "demo" records, tapes, and CD's over the years, showing off their best installations with top-notch players at the keys.
I guess in reality, this project is more fun to talk about than to actually do! I am always curious about the samples used in a particular organ, and have actually spent time listening to the 10-second snippets that demonstrate all the available samples on the Allen DOVE CD. Fascinating to note the subtle variations in tone color and articulation. But such curiosity is not much of a substitute for listening to real organs in person played by real people!
Church: Allen MDS-45 with Allen MIDI-DIVISION-II expander
Home: Rodgers 580 "Cheetah" organ with custom 6-channel speaker system
Shop: Bunch of organs in varying conditions, some good, some not...
Half of an incredible two-man organ service team -- servicing all the major digitals in Arkansas churches