They work different because we wanted to avoid forcing administrators from having to go through multiple vBOptions, ticking potentially hundreds of boxes, in order for their forum to continue to operate as it did prior to installing the modification.
Imagine you are running a forum with 100 usergroups, because you're running a gaming clan forum that spans multiple different games, so you need fine-tuned permission control. You want to ban new clan members from posting links in PMs. There are a total of 10 usergroups that belong to "new clan members" for the various clans.
Scenario 1: You have to tick 10 boxes in 5 different settings in order to ban "new clan members" from posting links.
Scenario 2: You have to tick 90 boxes in 5 different settings in order to allow "full clan members", as well as all your staff, to post links.
I don't think you'll find anyone who would claim that Scenario 2 is the most user-friendly scenario.
Scenario 1 provides the most user-friendly experience for new installs.
This is why the setting was created in a backwards way.
PS: It's funny you should bring up our Thanks mod, considering the most frequently asked question from new customers is "I installed this mod and nobody can click any thanks button, where is the button to click thanks?" because we employ Scenario 2 in that mod.
There has literally not been a single week in recent memory where we have not received that question. It costs us, as well as our customers, time and money as a result.
The customer is frustrated because the modification appears not to work, so they feel like they have wasted their money.
We are frustrated because we have to answer the same question eleventy bajillion times.
I'm sure there's a way to solve this that works both ways, but thus far I haven't been able to think of it.