I looked into it more after posting and apparently it will remain UL certified as long as the retrofit kit is UL certified, it will keep it intact for the fixture. So you should be good there after all. Now I'm not an electrical pro so do not take my word for it, I try to understand as much as possible but I may not be correct always.
Now adding holes into fixtures and such where they weren't designed violates UL ? Looks like some of us on the site are guilty of that including me! where we either mod fixtures or build them from scratch and most members do a (...) good job too!
I still don't feel comfortable having mains connected directly to the sockets, its just me though, because what would happen if someone put a fluorescent back into it, even if N and L were at opposite ends ? For me using LED tubes designed for the ballast allows for quick swapping back to fluorescent. Its more for the brightness than to save energy. The fixtures are using about the same wattage as they did with 25w F32T8 lamps but have more brightness than a 32w T8.
At the end of the day as long as your comfortable and happy with your setup that is all that matters! 
UL will void certification for a fixture/device due to mechanical modification because they can't be sure you haven't provided for continued ground protection (which is one of the major factors for UL certification: an enclosure that protects the user, i.e. proper grounding or isolation, you may be violating that by drilling holes or re-working metal). UL will also void certification because a modification/drilled hole violates the environmental resistance, such as drilling holes in a 4R box will de-rate the box.
UL looks at it like this: 120v goes into this "thing" and this "thing" has to be engineered to provide a reasonable amount of protection to a user. Grounding, isolation, touch safe, etc. Whatever happens inside the device is usually going to be contained by the engineering criteria of the aforementioned attributes. For example, a careless electrician leaves an exposed wire after a ballast swap...UL doesn't certify that a ballast swap will be done correctly, UL certifies that the fixture will protect the end user, either through grounding and/or isolation. I am just talking about one "thing" UL cares about, they have additional criteria to evaluate that doesn't add to this particular conversation.
Also, voltage is at the tombstones even with a ballast installed, and installing a fluorescent lamp on an opposite end fed ballast bypass won't damage the fluorescent lamp, at least not in the USA.
That all said, it depends on what you are comfortable doing. I can see why you prefer ballast-compatible retrofits. But, me personally, I don't mind cracking open a fixture and re-wiring it. easy-peasy. I will leave the ballast in the fixture with enough wire to re-connect if I change my mind. I just don't like to leave the ballast in the circuit when it is not needed.
I wouldn't worry about violating UL in our hobby. As long as you take care to keep the fixture safe, you can do whatever you want. Keep your fixtures grounded and wires isolated and you'll be good, modify away!