Do what is required of you, first and foremost. If you can't, it's time to update your resume and move on. Rebelling against shop standards is not a hill you want to die on. It will give you a bad reputation in the industry.
If you are convinced that there are better ways of doing things, design them on your down time and then demo them to your superiors when you have a chance. I assume you're young and fairly new to the industry (less than 5 years). If that's the case, you will not be taken seriously by the more experienced people on your team unless you can actually show them something.
In theory, they've every right to be telling me how to do things, because it's their department, their rules. But I'm strongly inclined to refuse to just do what I'm told, particularly if I can justify better ways of achieving the same objective.
This is a big red flag to me, because 1) It's not theory, it's reality. You are not the one who will be held to account when things go wrong. 2)It demonstrates a bad attitude on your part.
For the sake of argument, I am going to take everything you say to be absolute truth:
Shops need to adhere to standards. I would take a mediocre coder with a good attitude any day over a highly skilled coder who is willing to ignore the rules because he knows better. My other coders won't be able to maintain the code, and the highly skilled coder is employing new ways of doing things that the rest of the staff will be completely unfamiliar with, requiring retraining, expose the company to risk, as the old staff will be in unfamiliar territory, and thus prone to make mistakes.
Given all that, the highly skilled programmer would not be an asset, but a liability.
The simple answer to your question is that you do back down. It's not your place to oppose the company's shop standards. Get more experience, rise up in the company, do some development in your down time and demo it if you're that confident, but do not disrupt the shop standards because you have ways of doing things you believe are better. Even if your methods are better, they will be a disruption. Convince management through authorized action, not disruption.
If you are concerned about being told to do things in a way you feel are wrong, create a paper trail. Do what you are told, but send an email stating your concerns. "In implementing this, I have the following concerns..." then lay them out. If they say do it anyway, it's on them.