[Xposed Framework Modules] claytonjn:
The simple answer is because people install things without reading, it breaks other things, and they blame other people causing headaches for devs trying to fix problems they have no control over. By forcing someone to configure the app it forces them to have some knowledge of how it actually works. This is XDA-

Developers

after all, not XDA-EveryoneWhoKnowsHowToUseGoogleSoTheyThinkTheyAreKnowledgableEnoughToUseEveryHackTheyCanFind.

Obviously no two people have the exact same apps installed or use their phones in the same way, but in reality, how many apps do you really have that act as handlers for specific links? In general, those are the only apps that would have this problem. So you have Tapatalk, your browser, the Play Store, maybe a handful of others, but out of maybe 200 apps you probably have 5-8 that would actually benefit from this app. After only a few days you should have everything added and won't ever have to worry about it again, unless you install a new app that can handle specific links.

Do you have any proof that the unexpected behavior rarely happens? In just a few days there were numerous posts both here and in the SuperSU thread with people complaining that things were broken. As this module gains popularity that will only get worse, and that app is only one example.

Now, you're complaining that the new version is going to be all sorts of work for you. Well first of all, if it's so much work, simply don't use it. Obviously that isn't the decision you're making so you must think it's worth the work. But you don't want to put in the work, even though it's worth it. You probably feel it would be easier for GermainZ to have it as it was before, not really much more work for him, and less work for you, right? The problem is, if he's spending all his time repeatedly telling people to read the OP or use the whitelist he won't be using that time to develop other awesome modules.

One last thing to consider. I'm a moderator for the Xposed Repo, and as such I have talked to rovo89 numerous times about his feeling on what modules should and shouldn't do, etc. From what I gather, his single biggest fear is that a module will cause somewhat of an "uproar" in the general Android community (i.e. devs on the Play Store.) Right now Google is looking the other way and not doing anything to block Xposed from working, but rovo89 himself has said they could EASILY change things removing all ability of Xposed or anything similar. So if devs in the Play Store start getting complaints that their apps aren't working properly, spend hours hunting things down only to find out it was because of something like this that changes core functionality of Android that they rely on for their apps to work a specific way, then complain to Google that they are wasting time and getting negative Play Store reviews, Google would almost definitely lock down Android so things like Xposed are impossible.

Moral of the story; put in a little extra effort so that the developers can focus on developing, and if someone isn't knowledgeable enough to configure a mod/module they are trying to use it's a pretty good indication that they shouldn't be using it.

EDIT: By the way, one last thing to think about: nearly 15% of the posts in this thread are GermainZ recommending people to use the whitelist.