I see your issue but I must admit I've not had any queries from Users about using the filter scroll feature for longer lists. Usually filters are contextual lists which the user community should be familiar with. e.g. Country. or short enough to fit the constraint e.g. types, status.
Perhaps if you are worried people will be missing out on filterable options this is an opportunity to put those options in a different kind of visualisation chart e.g. a heat map for example.
I chose to do this with my Activity categories for this exact reason. I didn't believe users would necessarily use the scroll as per your highlighted issue so I wanted a way to make all these options visible to the user. I used heat because I could Weight the options so the higher the value the more important the option appears to the user.
I know this is not the answer you are looking for but hopefully this is an option/approach you can consider.
Regards
Andy
