Hello stevejobsfan0123,
There is more to SIP than just protecting directories. It is true that a developer that relies on modification of system paths is likely just incompetent or lazy. But you can't really make that determination without analyzing each specific app in question. Some software will run just fine /usr/local, in that case, there is no point in trying to modify /usr. But if the developer is actually trying to modify some existing Apple resource, executable, or config file, then modifying a protected directory might be the only way. (But usually there is always another way.) And to tell the truth, it is only a few particularly nasty open-source libraries and Perl modules that are the biggest offenders here.
The other, more important component of SIP is protecting processes. This is probably what breaks TotalFinder. Here is slightly more information: https://developer.apple.com/library/mac/documentation/Security/Conceptual/System _Integrity_Protection_Guide/Introduction…
The key part to remember here is the audience. People hear something like "System Integrity Protection" and think it is some kind of security architecture to protect them. It isn't. It is security protection for Apple, not for the user. (See: About System Integrity Protection on your Mac - Apple Support). What does SIP protect Apple from? Malware, certainly. But it also protects Apple from legal and legitimate hacking, illegal hacking, and, last but not least, the user himself or herself.
Does this mean that disabling SIP is wrong or risky? Not really. Considering the fact that El Capitan has SIP enabled by default, those system directories are protected by a technological version of "herd immunity". No halfway decent hacker would choose that path of attack, so the presence of SIP on most machines even provides protection to those people who keep it turned off. You would get virtually all the protection against malware, but none of the restrictions.
As for me, I keep SIP turned on. If I were into hacking, I would just use Linux. But I reserve the right to change my position in the future.