Back in the day Tekken had community written rules / restriction for tournaments.
StarCraft (all of them) has always had patches that tweak balance and adjust whatever they feel is "too good" every so often.
World of Warcraft had patches that significantly changed balance, I'm not sure what they do now.
I don't know how they handle League of Legends, but I'd probably bet they patch in balance tweaks every so often.
These are some of the most successful competitively played franchises ever and they tweak the rules to make competition more fun. Almost all of them take the "top down" approach as well.
Unplugging, some of the more prominent example of game companies (or affiliates) adjusting for balance include Privateer Press releasing semi-frequent "patches" or FAQs / errata that straight-up CHANGE things. Magic the Gathering has a banned list that's updated 4 times a year. Sometimes the updates contains no changes, sometimes they unban a card, sometimes they ban what they feel is the "broken piece of the puzzle." Some people cry, some people cheer. /shrug
Do these changes sometimes have a substantial effect on the metagame? Sure. Unfortunately all of these companies (except Privateer Press) have TONS of data to base their decisions on. Do these balance related changes upset some people? Sure. Do some people stop playing? Sure. Is it usually for the better? Debatable. Does it "fix" what's "wrong?" Sometimes. Is it okay? I think so.
Does it set precedent? I guess so, but people tweak the rules for their local events all the time, right? Comp stuff and all that, 2x FoC or not, etc. Might it start a period of community re-writes a la WHFB? Probably. Is that going to happen anyways? I think so.
At the higher levels it seems that 40k is in an odd place right now. GW (rightfully or not) doesn't seem to give a fuck about the vocal 10% and is sticking to their mantra. It's strange. Do we as the community sit there, smile, and hope... Or do we try to change it? The "hope" route is an interesting option due to the rate they're putting out content / product. The "change it" option is tricky because GW might fix it on their own next month. Do you take the chance and spark this kind of debate, which clearly creates some kind of rift, or do you just continue to let it go?