Right now, if the input portion of a rule contains a specific tile, that tile will not count as nonEmpty. Take this rule for example:
(region + input on the left, and region + input+ output on the right)
This rule outputs this result:
However If I change all the surrounding tiles to a tile that is different from the input tile, the rule seems to work. Like this:
Is this expected behavior? Is there a way to make NonEmpty inputs accept other input tiles as valid NonEmpty tiles?
Is the magenta area in your rule a regions layer? If so, delete it: regions are not needed in 1.9+ and are only included for backwards compatibility with pre-1.9 rules (before the special Automapping tiles existed), and they trigger pre-1.9 Automapping behaviour. I think you’re actually running into the old behaviour that if a tile is empty on all input layers (and I guess the special tiles get ignored in this mode), it counts as “Other”.
I just set up an equivalent rule to yours but without regions, it worked correctly in both scenarios.