Like others have said, we're likely going to see a Markakis–Acuña–Duvall alignment starting Friday; this is sub-optimal, in general, since it means Duvall regularly faces RHPs, and Markakis occasionally faces LHP starters and likely sees LHP relievers in key spots. It's also not the ideal defensive alignment for the OF. But obviously the Braves feel as skeptical as you that Pache can hit better against LHP than Markakis—who, fwiw, has actually killed LHPs this year, to the tune of 161 wrc+, versus 136 wrc+ against RHPs—so they're willing to make that "sacrifice" (along with the legitimate defensive sacrifice) and keep Pache down. This is probably the right move, tbh, given the paucity of LHP starters the Braves face this year, and the benefits of further delaying Pache's service time, plus having him regularly work on things at the alternate site, as opposed to riding the bench.
Obviously, they also feel Duvall is a better option against RHPs, even given his below-average career splits (91 wrc+ career versus RHPs), because he's at least got the power to do some damage (.460 SLG in his career versus RHPs); he's also been slightly above-average (104 wrc+) against RHPs this season—so, again, this is probably the right call.
The bigger, looming question is what to do with / about Inciarte. He's fine as a defensive replacement for now—his defense hasn't been as stellar as in the past, but he's still above-average, and late in games it's probably better to have him in CF, Acuña in RF, Duvall in LF, and Markakis on the bench. But next year is an entirely new question—and I have to admit, despite being a Inciarte defender (or, at least, a firm skeptic of a bottom-falling-out total decline), some of the numbers are starting to look abysmally worrying:
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Sure, even in those very good years now in the rear-view, his EVs were only around 82-83 mph. But losing a full five mph from that—falling sub-Foltynewicz in terms of hard-hit balls—doesn't seem remotely viable for major-league PAs. Like, maybe Fried should hit and Ozuna DH for Inciarte-territory.
Don't think there's any question that Pache is the 2021 Opening Day CF at this point - the only question is whether there's enough financial flexibility to DFA him this winter if someone won't take on any of his salary (can't imagine anybody cares about the return). With Pache AND Acuna on the roster, it's awfully tough to justify giving him a roster spot - even if his defense wasn't declining.
I get not having Pache on the roster with Markakis and Duvall around this season - they've both over-performed expectations against same-handed Pitchers, but it's all but impossible to imagine that there's enough money available to bring them both back (at whatever that might cost) while hoping that luck continues - AND pay Ender to sit beside Culberson for 6 months.