The Lake Trio being regionals that didn't change spawn territories from last time (which is its own can of dumb to me) means they were going to encourage more Remote Raiding than usual, at least among collectors who would do them en masse to get a Shiny that now wasn't showing up when it should. This would have made more sense to sneak in during a relatively low value Raid rotation like Regigigas.
When there's a limit of 5 remote raids a day, you can't exactly encourage more remote raiding than usual; hardcore raiders probably do that many raids fairly frequently. And it's not as if they really hyped up the lake trio being in raids at all: it was just part of the general June content update "yeah these will be in raids for a couple of weeks". It wasn't like they went all out with "can you catch all three of the lake trio?" or anything of that sort.
Granted, they could have swapped them like they did with the legendary beasts initially, but Niantic seem unwilling to do that for whatever reason (probably because the very existence of remote raids makes doing such a thing fairly pointless).
So I don't really think they were trying to encourage more remote raiding, beyond a couple of token boxes which didn't really give much of a discount; if they were they'd have probably raised the limit on passes.
(Also do we know for sure it
wasn't snuck in during Regigigas? There was an issue with Kleavor's raid day where the shiny rate seemed to be far lower than the expected 1/10, documented in a similar manner to this - personally speaking I did over 20 Kleavor raids across 4 accounts and got one shiny, but hey I just figured I was unlucky. I can't imagine people were doing anything like the same amount of Gigas raids so maybe it got overlooked. Idk though.)
If Niantic intended this to further kill Remote Raids, I feel like they would have publicized it, whether truthfully (they haven't cared about saying controversial things before with regards to "Play Local Raids, we don't care about the complaints") or trying to spin it a certain way ("Local Raids will now have a Bonus to Shiny Encounter Chances over Remotes" which is technically true if they stay 1/20 and the Remotes drop to 1/100). They don't have any intention of weaning people off Heavy Remote Raiding, they're trying to push them to quit near-Cold Turkey and go back to Locals with the Shadow mechanics and meager in-person bonuses
Why would they publicise lower shiny rates, though? This way, people still buy passes. If they'd said "Uxie, Mesprit, and Azelf obtained from remote raids cannot be shiny" that'd be one thing - this just reads as them going "well, if they're still going to buy remote passes, we may as well make more money off of it".
The fact that they bothered coming forward to admit it can be read another way to me, as deliberately done or not, they probably are concerned enough about PR to not want it framed as them fixing the odds under the hood, since that reflects a LOT worse on consumer trust and hurts their future business prospects as well (which they obviously are concerned about considering Niantic and the PoGo Twitter account likes to retweet messages from their other games).
Go Fest is upcoming, so yes, they probably are (more) concerned about PR and looking good (than usual). The compensation offered goes far beyond what they've previously given (usually it's "you'll get 1-3 passes" even if you did 20 remote raids on something bugged). I've already seen lots of "wow, this is really cool of them" comments from people. If this
was deliberate, it's kind of a win-win as now they get to look all magnanimous.
There is a marked difference between "your customers don't agree with your business decisions" and "your customers actively do not trust your product or business" as problems when pitching themselves to investors or collaborators.
Has this... ever not been the case? No, but seriously. It's a long-established trope at this point that Niantic are incompetent. I know very few people who would be likely to say "I trust this product". They might like the game plenty, but no-one I know is surprised when there's some sort of bug or outage. Yeah yeah, "never attribute to malice what can be attributed to incompetence" and all that -
this week alone they fucked up Sandygast's release as well as Shadow Sawk and Throh. So I'm perfectly happy to believe that this really was just down to pure incompetence with no greater plan to it. It just strikes me as a massive coincidence that this particular flub coincides so neatly with their desire to discourage remote raiding.