No, those scripts will not be updated because those tables are no longer needed and people still have them. Data in this community has the way of sticking around, and confusing people years later, so this is my way of purging the system
Just source with verbose mode off (drop the -v) and it'll skip right past them. *Releases will not have this issue, only tables contained in the release will be sourced/droped*
rule_values is a player script because it is a table commonly changed by the end user. Having it as a system table would piss people off with tweaked rulesets. Having a third category is not an option because I am too lazy to update PEQ's script, and quite frankly having two scripts confuses many people as is, adding a third would make matters worse.
Yes, any and all tables can be sourced in separately. rule_values, commands, variables, etc. I don't recommend doing this for system tables because obviously many tables are linked together, so sourcing in one without the other will create errors and/or features to not function.