All good questions. Apple's end game is to push for app's they approve via the MAS. If an app gets into system [root] settings, they won't approve it. Using SIP will deny its use, thus forming an end game. Either the developer abides by set rules via the MAS (OS X Mac App Store) or the app/developer folds.
As Apple takes 15% off Apple Music profits, they are following suit with the Developer Revamp (15% instead of 30%). Instead of paying $99/year for separate iOS and OS X development accounts, $99/year will cover both to encourage more developers to use Apple's conduit. The potential increase in app sales would outweigh the 15% Apple decrease in revenue and possibly may surpass sales by "locking down" system resources for the sake of improved security. It's a win/win.
Since the MAS's release, overall sales haven't lived up to internal expectations. Many developers have come forward along with research/figures to support the fact the profits aren't as impressive as many assume. Thus many developers push their apps independently (and via the MAS if approved) in order to bolster sales. Top ten "Paid For..." doesn't necessarily mean the developer is making decent, or even reasonable, profits. It's a bit of a misnomer.
Marketing has been developing methods to entice developers to utilize the MAS. SIP and lowering Apple's percentage being two convenient means, many others are on the table. Additionally, aside from boasting YOY records compared to iOS sales, it would allow Apple more control over what app's are approved as OS X engineering has sidelined proposed core system features that some developers have already implemented. This is mostly frustrating as unforeseen applications made it difficult to implement similar/exact key components into OS X. As OS X is a tightly integrated system, one key feature that depends on another which is either available third party and/or via MAS (approved without foresight) has resulted in sidelining many projects. Cannot name it for obvious reasons but some will know it, one app in particular that adds an iOS style panel similar to Notification Center resulted in engineering placing this feature on hold. This OS X feature was to be integrated with iOS devices akin to Handoff and Continuity.
There are many reasons for Apple's desire to better control third party app's running in OS X. As they have no direct [legal] control regarding non MAS third party applications (including pirated apps), which may result in security comprises to OS X feature integration and lower than expected MAS sales, SIP and possibly locking out third party application installations may be the steps towards these goals. Currently, allowing apps downloaded from the MAS is the default setting in OS X. That may change once Apple formulates an enticing prospect for such developers to utilize their system, thereby lessening possible outrage.
Again, this is all hearsay and I never wrote this and I love your app.