I have reviewed this mod with a pack of AAI mods & Miniloader mod ( https://mods.factorio.com/mod/miniloader )

That what I found:
1) If miniloader in the split lanes mode (click on a some miniloader, it should be configured to OUTPUT direction - place a belt in front to it; in the popup you can see the "split lane configuration" at the top panel)
So if the miniloader has a configured different signals for separate lines, then it will replace the common/left line signals, but the right lane signals will be ignored from the replacement process — it leaves them as replaceable variables there.

2) It does not replace signals in the (invisible) AAI Depot Exchange Data (entity name = "vehicle-depot-combinator"). Possible it requires update/set via a some interface method from AAI mods.

Could you add support to these mods?

I will add that to my list! Thanks for the feedback!

I'm not able to select variables to be filtered in miniloaders (which is expected, I'm not sure how you can...). Also, the split lane configuration pops up but I can't individually filter left & right, only left OR right. Are we using the same mod? Am I missing something?

Regardless, this will be easy to fix once inserter filters are done. I've added it to my list of things to support.

Regarding AAI Depot Exchange Data, unfortunately the mod is deleting then replacing the entity without raising script_raised_built or script_rasied_revive. Turning off your personal roboport, applying variables, then turning your personal roboport back on is a workaround. I will look into submitting a PR to AAI programmable robots.

It's on my list of mods to support, so if I don't get any movement, I have a workaround planned.