For many items like ovens or anvils or buttons, it makes sense to have flags because some harm is done when they are used. However in the case of enchanting or crafting tables, there's no ill effect that can happen from allowing others to use them. The main advantage of allowing them to be used by default would be decreased frustration for new players who want to allow others to use them and less problems where people have spelled the sign incorrectly or placed it in the wrong place or don't know it is needed. In addition, signs contribute to lag and it takes time to set this up. Consider also that some people set use flag to true to avoid having to configure each crafting table or enchanting table individually, and might not realize that they are putting themselves at risk if they have some redstone elsewhere that someone could use. (Or they forgot about that redstone device, or they forgot about the global use flag when they added the redstone device.) Correct me if I'm wrong, but I can't think of a case where someone would want to disallow people from using crafting or enchanting tables on their residence. Seems to me that if there is a case it would be very odd, and this is only being an inconvenience to most players. So it only makes sense to allow them to be used by default.
Are you talking about the flags? You are asking for something like ./res pest (player) furnace (t:f) -- ./res pset (player) craftingbench (t:f) If that's what you are asking, I personally don't think there is a need for more flags, and if you may elaborate a bit more to what you would like to see. As of right now I don't feel anything is wrong.
I could have sworn I was on a res and it said I couldn't use a crafting table recently, but I can't seem to find where it was.
This should not be the case - the flags were eliminated a while ago as stated above so you should be able to use crafting and enchanting tables on any residence, no matter what. However, if this is true and you cannot use the mentioned tables then something has gone wrong as you should be able to use them, even on other people's residences. If something has gone wrong then you can always send a screenshot to staff and it should get sorted from there!