Cassettes are a pain. Head alignment is extremely important for analog tape fidelity, and it's always off for home recordings.

With pro analog tape recordings (e.g. 2-inch 24 track, half-inch 2-track), you record alignment tones onto the tapes to capture the state of the recording device, and then later calibrate the playback device to the particular tape so that playback alignment matches recording alignment. But this is essentially never done with cassettes, so you have to earball it.

Cassette players for mastering studios actually have alignment options (e.g. adjustable azimuth) that aren't present on consumer devices. But without the tones, you have to guess.

The problem with starting from a digitized source is that it may have been digitized from non-aligned playback. Ideally you want to go back to the analog originals - but old cassettes are rarely in perfect condition.

Both.

Grateful Dead has analog reel-to-reel recordings going back to the 60's but most of those have been digitized already or are in the Deads vault.

There are also large collections of recordings on Betamax cassettes made with Sony PCM-F1 digital front-ends which were used before DAT become available. These are digitized versions of old analog recordings and original digital recordings from the 80's. They need transferring and sample rate conversion (they are 44.056kHz) and in some cases pre-emphasis removal.

There is also a lot of digital material on DAT cassettes including analog transfers and digital recordings from the 90s. There are also some CD-Rs where original sources can't be found.

A lot of the cleanup is just figuring out what comes from what show and substituting sources where there are gaps to make complete versions for listening. The archival nature of the endeavor usually limits the amount of "clean up" that is done.