Hi!
Sure, you can set the appearance of the taxonomy term filters, as well as the checkbox default statuses here: https://i.imgur.com/m4lvfCj.png
The custom fields part should work as well, as the ACF fields are auto-detected and requested from ACF directly. There are actually 3 redundant methods to handle those fields, but yet it still does not work in some cases. I noticed that it has something to do how ACF loads on certain pages, depending on the page type. We researched the whole web for this, some other devs had similar issues, but no solution to it yet, it is so inconsistent.
Some pages have the issue, some don’t, it also depends on the data type and many other things, it is really a nightmare to debug.
If it’s possible, I would rather suggest using the taxonomy terms.