Fix check_output_custom uses applies_to

[jernejfrank]

#1658 added docs that flagged discrepancy between check_output and check_output_custom. The latter never used the abc method applies_to to verify it can actually validate the output based on the node type.

Added this as an if conditional, so it only applies it to outputs of the same type in case there are multiple. Alternativelly, we could raise an error instead of silent behaviour but not sure how much benefit it gives.