Most php syntax files work with phpRegion and use php or html syntax as appropriate. With Rainbow Eanbled, it all become php.
for example, without Rainbow:

After :RainbowToggle:

I'm not well-versed in vim's syntax code... but i can see that it already includes containedin=@htmlPreproc which should have limited these synIDs into the php region...?
Most php syntax files work with phpRegion and use php or html syntax as appropriate. With Rainbow Eanbled, it all become php.
for example, without Rainbow:

After

:RainbowToggle:I'm not well-versed in vim's syntax code... but i can see that it already includes
containedin=@htmlPreprocwhich should have limited these synIDs into the php region...?