I'm aware of the fact that it is the amount of ambient light getting to the sensor determining the brightness of the background. However, there are several ways to achieve this (e.g. lower F value). It is also possible to increase the sensitivity setting (=higher ISO) to get a similar effect.
The difference between changing the shutter time and F or ISO is that the latter two affect both the ambient and strobe light to the same extend. In contrast, shutter time only affects the ambient part of the lighting because 100% of the strobe pulse will be captured even at the fastest shutter.
In my experience the only reliable way to remember all the little things that need to be taken care of is to actually take an image when the camera setup is complete, including flash. It doesn't help you remember to put a diopter on a lens that needs one in a dome but takes care of most other mishaps. Of course the problem then becomes to remember to take that test shot. Oh, it also helps to not put your wetsuit on backwards. Been there done that
If it was me I would prefer the filter right on the lens because, unlike diopters, there is no great incentive to take it on/off as needed. The only conditions I can think of where you may want to take it off is in very shallow (<2m or so) depth or perhaps when shooting in B&W mode. But in both cases having the filter in place is not a big drawback unless natural light is in limited supply.
The 12-50mm port will also take care of the macro lens or you could get the macro port which will also take the 12-50. The latter is a lot less money but you can't use the special macro mode. There have been a bunch of recent posts on wide angle prime and zoom lenses and their best ports. Just look for Phil Rudin and you should find all you need and then some.