We have also run into this issue and took the same measure (disabling Safari) to temporarily stop bad behaviors.
We noticed that on the iOS devices, the web content filter restriction is pushed, but there are no filters applied. When deployed direct to a device using Configurator, the web content filters are applied appropriately.
Looking at the config file from Configurator (v2.15), Apple is still using and supporting the WhitelistedBookmarks key. The issue is that per the Apple developer docs (WebContentFilter | Apple Developer Documentation), they're supposed to be using AllowListBookmarks now (with WhiltelistedBookmarks being deprecated), which is what Meraki SM has apparently switched to using.
I manually updated a mobileconfig file to test the AllowListBookmarks key and pushed it with Configurator. It broke in the same way as if SM pushed it.
Looks like there's no quick answer here as Apple will probably roll out support for the new key at some point soon (maybe 15.2?), so not sure if there will be a fix in SM for it.
In the mean time, we'll be testing a stop-gap measure by manually creating a web content filter in Configurator and deploying the mobileconifig file using a custom Apple profile. Hopefully, I won't have to have 2 settings profiles for devices pre and post 15.2 (or whenever they switch)...