Weeeell.... that's assuming it wasn't a decision made based on (unexamined) assumptions about the way things worked.
This isn't intended as a sleight against the work done back in those days, by the way. There are enough examples in the forums of the same cropping up and biting my ass as well (Re: do you need to Item History "blank" key knowledge ranks on a thread item?), so I'm hardly one to talk.
To answer the question, at my table I've generally applied penalties to "action" rolls as well as "effect" rolls, if only for consistency and ease. After a little bit of consideration, I recognize the point of view of the arguments on each side, and I don't think it makes a huge mechanical difference one way or the other, as long as you're consistent at your own table.
Which, yeah, doesn't make it any easier for somebody trying to code a character sheet for a VTT, but... *shrug* I've got other plates in the air.