So far from my experience, the order doesn't really matter. I haven't come across any situation where the order causes strange stuff - even with multiple 100 codes it seems to work fine.
I guess it's because the list is used in an AND filter. I.e. one of the DXF codes in the entity MUST clear every one of those tests in the filter. But when you start using the -3 codes (i.e. more complex boolean stuff) the boolean logic imposes its own precedence - so then order would be of consequence.
Edit: The above sentence is ambiguous. Here's a better one:
Every item (or group of booleans) in the filter list must be found in at least one of the entity's DXF codes.