It will in no way disadvantage the battery health. On the contrary, for the remaining time the system thinks there is a weaker battery it won't let the new one discharge as low so it would do the opposite of what you claim, contribute to a longer life for your new battery (albeit only for a few hours till it relearns).
The only owner disadvantage is for a short period the battery saver circuit may kick in sooner, owner may still see the battery warning message mere hours until it accumulates more data points to adjust the battery profile.
IF for some reason, you have a situation where the system never relearns, doesn't go through the hourly cycle and you find it annoying that it warns of low battery, then yes reset it. This does not affect most owners and should be considered a wait and see situation.
Please provide data demonstrating your claim instead of speculations following 3rd hand interpretations. Data means voltage and current readings, not repeating things others have misinterpreted.
I'm going by the workshop manual, although the general premises apart from a BMS-specific application you've stated here I do believe are ones I also trust as correct. Per the workshop manual--although it does state it differently depending on which one you look at (Taurus vs. Explorer, etc.)--the Body Control Module will treat the battery as in an aged state without a reset. This affects the charging strategy including how aggressively the battery is charged based on ambient temperature conditions, inferred battery temperature, and the availability of regen (idle coast down) charging. If there's some data out there comparing system performance (alternator command, etc.) between a new battery thought to be aged and a new one after a BCM reset, I'd love to see it--nobody's ever had the data to share, and I'd love to learn more about the system as well. The WSM only scratches the surface on the underlying algorithm. I've watched a small piece of it in action with a ScanGauge but not enough to learn what I had hoped.
So, yes, by resetting, you're resetting the inferred battery life % (in my experience it seems to "set" at 80% until it truly recalibrates) that it draws from the Hall effect sensor, and thus avoiding a load shed problem if any existed. If not, yes, you have to wait the 8 hours per the WSM to come back. But the downside to doing that is you're losing some efficiency designed into the system to maximize the value from a larger battery--so ignoring the reset isn't as fault free as suggested. That was my main point, however minor it seems to most people in the grand scheme.
As far as battery health, I shouldn't have put that--I flippantly put it as "or otherwise" as it doesn't make sense to me that a new battery wouldn't be at least slightly disadvantaged by the less aggressive charging strategy. In your narrative, you suggested it wouldn't be discharged as severely. I've never read that in the WSM, though I would believe it possible. The discussions I've read on the topic seem to infer more about charging up rather than how how the discharge looks. For example, when the car stops or nearly stops using regen charging based on age, etc.
Do you have any graphs or data points? Not to challenge, simply to see more/learn.
Cheers.