Yeah, I agree with john and what you found out, to be Paralell to the pick guard you dont have to be flush with it.
I think with the case of stock Ray4 pickups, you can definately lower ygem a bit to overcome some of the hotness, and wherever it sounds best you can go with.
If you actuallt thought flush sounded best, that would work
Like you said, no thumbrest.
Plus you can lose a little bit of tge percussiveness you get from plucking over the pickup, even using the pick up as a finger ramp, like I do.
You can add a thumb rest to have a place gor your thumb to anchor, and / or add a finger ramp to get some percussiveness back, and even use the ramp to anchor your thumb.
You can do whatever you like best, as long as it sounds good TO YOU, and is comfortable to play, both gor your thumb and plucking fingers.
Its good you are experimenting, and better you are reporting your findings.
It would be cool if you can find your favorite pick up height, and offer that as anotherway for new Ray4 owners to get tge most out if tgeir new bass, OTHER THEN to recommend a new pick up right away.
We all know the potential the Ray4 has as an upgrade platform, but it will be great to get a good set up ti let new owners enjow the new purchase, without having to automatically drop in a $50 to $150 pick up.
Especially people intimidated by DIY projects, that would incurr a $40 and up charge from a music store, instrument repair shop and or luthier.