In vanilla 2.0, all inserters can be configured with up to 5 filters. Currently with only Ultracube and it's dependecies enabled it seems bulk inserters can only have 1 filter and long arm inserters can't be filtered at all.

It's intentional.

This creates a problem when upgrading blue inserters to green ones. The inserters that had more than one filter silently lose any filter settings beyondthe first.

I would suggest that all inserters should have consistent settings (though dropping blues to one filter slot would now break my base), or at least should not be auto-upgradeable (similar to how Space Age makes bulk inserter not upgrade to stack inserter by default).