I fully agree with your preferred behaviour. I think no. 2 and no. 3 are a must.
You're correct that the "mini-bar" could disappear in scenario no. 1, because seeing two different progress bars at the bottom of the screen at the same time might be confusing.
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Unrelated suggestion (cosmetic): in the fabulous XHTML output of highlights and notes (Marvin's
no. 1 killer feature for me that makes it clear Marvin is superior over Stanza, iBooks, the Kindle app, and the rest), could you please stop adding a period (.) following the time-stamp? It's
great that the notes are time-stamped (another among countless clever innovations in Marvin!), but the final period following the time-stamp doesn't make sense syntactically or typographically. Thanks for removing it, if possible.