It very strongly appears they took and modified straight Pokemon models, or at best used them as a direct reference.

No. Definitively no. The models aren't even remotely similar. Here's an example with Lycanroc vs. Direhowl, one of the contentious pairs:

• different proportions: Direhowl is considerably bulkier. Lycanroc has thinner legs and belly
• some parts don't have good analogues: Lycanroc's fang is missing, Direhowl has a rather detailed nose, tufts of hair on its back legs, and a tuft of hair between both ears.
• analogue parts are shaped differently: best seen with the neck fur - Direhowl's is fluffy, Lycanroc's is spiky.
• the number of points of any part simply does not coincide. And it's hard to claim that Direhowl's mesh was Lycanroc's minus a few points, because Direhowl has a lot more points near the extremities.

It would be literally easier to create a Direhowl-like model from the scratch than to distort Lycanroc's model this way. And that is likely what they did, they clearly did not copy Lycanroc's model. Similarities are simply easier to explain by the fact that both are inspired on wolves.

Same applies to other pairs of creatures.

If you want to see how reused/copied models would look like, check this. It's from an old controversy where GameFreak lied to the players that they had to redo the models from the scratch, to justify Dexit.