The larger sensor cameras will have much less depth of field which will always make macro focus a more difficult proposition regardless of the brand. The 90mm lens will be challenging. A better bet is the kit lens with the Nauticam CMC-1 or CMC-2 for starters or similar wet macro lens and work up the 90mm macro.
The TG has a sensor the size of a pinhead and thus has huge depth of field allowing for less than perfect set up to squeak by. A M4:3 or APS-C and even more so a FF camera will need more skill.
Sony cameras including the A6400 have excellent auto-focus capability and if you will set up back button focus and center focus point you should do fine.
My NA6400:
You bought a more advanced and capable camera replacing basically a point and shoot snappy cam so now you will need to attempt photography. A more capable system will need more skill, practice, effort and even then, at least for me, my photos still suck, oh and frustration. And it is me, not the camera.
If your Sea Frog housing will not support back button focus, well, that would make me sad. You will need to rely on a half press to hold focus and I find that near impossible even with the excellent Nauticam trigger.
By default the Sony a6400 is not setup for back button focus. However, if you wish to use this method of focussing then it's really easy to setup.
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BBF is a game changer, at least for me. With BBF, you preset the focus distance and then move the camera in and out until you are at the prefocus distance and then take the shot. Or, hit the BBF and get your desired focus distance and then recompose to suit.
Turn off the eye detect and all of that, it just confuses my camera when attempting macro. To find the eye of a seahorse or nudi is asking a lot of the camera software.