if your startup ever makes it to any sort of scale, it will likely have the same problems -- they all do :)
The main problem is that the team has a lot of work to do. So simple tasks might take awhile if they aren't high priority. If I got significant push back, I'd talk to my manager or skip. Because doing it sooner would mean pushing back other high priority requests.
So don't break stuff. If you are google or aws then fine do what you want. There will always be another customer along soon.
but YOU are not google or aws.