How can I prevent WebKit feature flags from appearing in my iPad backup?

Where are you seeing this exactly?

Webkit is an open source web rendering engine. It isn't just used for testing websites. Safari runs on Webkit. It's required for Safari to work.

If your iPad is running slowly, the first thing I'd consider is a forced restart. You may also want to clear your website data: Settings>Apps>Safari>Clear History and Website Data.

Apple hides a lot of things from the end user. But there's nothing nefarious about that. Your car engine and all its attachments are largely hidden from your view. The only diagnostics you get without special equipment is a couple of lights on the dashboard. This is because most of us don't know a carburetor from a crocheted tea cosy and there's no benefit for us to see it.

If you don't know enough about how something runs to know what's normal and what's not, everything seems suspect. You have some choices. You can learn how it works but, as in the case of cars, it's going to take a fair bit of effort and study on your part to learn the skills necessary to understand how iPadOS works. Or, you can accept that things are probably fine.

I will add that you should not mess with Webkit feature flags; changing the wrong one can easily break all of the browsers and most of the apps on your iPhone. If you have changed them, go to Settings/Apps/Safari/Advanced/feature flags, scroll to the bottom and tap Reset All to Defaults.

Well, if they are in Safari they will be in the backup, so they can be restored when you restore the backup.