This would make sense. The point is, we will never know, as hardly anyone outside of Apple has insight on how they handle IPSW updates/installs. It could be that they compare file date/size between the IPSW and what's already installed, and just copy it if there's a discrepancy, essentially making it not too different from an OTA update. Or it may be as you say, and they replace everything.
In any case, as a further anecdotal data point: I never ever did my updates with IPSW. Always OTA. And I've been through most betas. My iPhone works perfectly. So it's not OTA vs IPSW per se causing (nor solving) issues - there are so many other variables in play.