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Both shops are partly right. The car has a battery sensor on the negative terminal that tracks capacity and age, and if you fit a new AGM without telling the module, it keeps charging for the old, worn battery. That shortens the new one’s life, so registration with a proper tool is worth doing.
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Swapped the battery on a Ghost a couple of years back and skipped the coding because a guy said it wasn’t needed. Within a year the new battery was already weak. Second shop registered the battery type and capacity and it’s been fine since. Ask upfront if they do it.
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“Fry a brand new battery” is dramatic. Skipping registration won’t destroy it overnight, it just ages faster because the charging profile is off. And the car won’t fully adapt on its own after a few drives, so the “just swap and drive” shop is cutting a corner.
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The sensor sends battery state over LIN to the power management module, which then adjusts alternator output, start-stop and even which comfort features shut down. Reset tools write the new battery’s capacity and chemistry into that module. Wrong type coded, like flooded instead of AGM, is the real risk.
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Which model and year is yours, and what’s the battery doing right now, slow cranking or electrical warnings? Also, did either shop say which tool they’d use for the registration? Older Phantoms and newer Cullinans handle this differently, so it helps to know.