why does it make it more difficult to properly block users from that instance?
Because on Lemmy at least, blocking (beyond individual users) generally isn't that effective. Doing so wouldn't hide users of a blocked instance if they posted in this community for example. Even community blocking is a bit weird... I often see image posts from a blocked comm because the image itself isn't hosted on that comm, though none of the comments will be visible (luckily in that case it actually isn't a big issue).