In aggregate, for a publisher, balance can matter a lot - it impacts the play experience of thousands. In particular, for my own game, balance is only a matter of a half-dozen people, and I've always felt comfortable managing it myself. So, if I'm lacking a sub-system, I'll generally just make it up or handwave it.
This approach would work less well in a game filled with rules-monkeys - the types of players for whom interacting with the rules of the game is a major source of fun. My players aren't apt to go deep into the details of the system I use for sailing, so the details of that system don't need to be particularly balanced. If I'm not using the subsystem a lot, I probably don't need it at all.
For me, I have too often been in a game where the DM hand-waved something that gets used over and over in game. At low levels or at the level the hand-wave was introduced it wasn't a problem. But as the game got towards epic levels, the misread by the DM on what the rule adjustment did to the overall system broke the game, as they hadn't considered the ramifications of what the ruling did overall.
Balance for me has little to do with 'rules lawyering' rather how it affects all the rules or other subsystems of the rules. One little change can drastically affect the overall game.
One way to look at it, as some people think PF is just a copy/paste of 3x, yet even the slight changes between those systems - there becomes a huge difference in play. They become different games because of the slight changes. The same is true with any hand-wave or rules adjustment.
A rules adjustment that turns out to be not well thought out can ruin a campaign... I've experienced that occurance in more than one campaign. One of our players was one of our former DM, after his consistently poorly thought out rules adjustments causing infinite amounts of problems in the long run - we don't let him DM anymore. (When he suggests he'd like to run another campaign - our group unanimously votes - NO WAY...)
I am normally a "right tool for the job" kind of GM. If what I'm looking for is not found natively in a system, then I look for a system that does have it. This goes especially for genre - most systems support only a small number of genres at their roots, so I'll generally seek out a system that does that genre explicitly, rather than modify another game to do the job.
D&D doesn't have sailing rules, and doesn't really do swashbuckling-style action well, and I want to do a game of pirates? Well, then I'll probably go look for a game in which pirates major thing natively, rather than use D&D to begin with. When I wanted to do "Wild West + steamtech + magic", I didn't look for a D&D supplement that handled it - I simply went straight to Deadlands.
Sure if you're looking for a completely different genre. When I described I needed sailing rules, we weren't playing pirates or swashbuckling adventures. It was just a vanilla homebrew D&D, but suddenly half the campaign occurred at sea. Having sailing rules tailored to D&D specifically made our game smoother and easier to run.
Usually when I need a genre adjustment its a small thing, not a completely different animal, so no need to switch to a different ruleset just for a slight adjustment or one extra subsystem.
Kind of the same reason I am developing Kaidan for PF. The core rules, as well as what I know about Jade Regent didn't fit the bill for my needs for an oriental horror setting. So I built Kaidan to fit that bill. I didn't need to switch to CoC or other game system, PF works fine, but needed a slight adjustment - Kaidan, for me, is that adjustment.
