Indeed I do run Q towers year round on my 03.5 (yes, you DO have an 03.5 if it's rackless) And I haven't had problems, hell I had the rack on my honda forlike 6years prior to owning this car, took it off maybe twice a year, and never had any paint problems (well except that it didn't peel under the towers like it did elsewhere)
Someone did adapt a set of Thule tower to mount with the factory setup, but the results are not what I'd consider desireable. Looks kinda goofy, and well if you odn't have a factory rack, you'll have to drill holes in your roof to attach one with (my g/f just swapped her 02's rack out with a canadian car's strips to make hers bare, and there were screwholes left now that had to be caulked in)
If you really just want a cleaner look, and intend to keep the car for ahwile, I'd just go all out and track it. I'd have tracked my civic if I kept it. it's the ultimate in easy clean multipurpose adapatable setup, but yes holes right through the roof. Railriders are the lowest profile smoothest towers you can run, Plus, you can pull 'em off and there's nothing but very low profile stips left. It all comes down to priorities.
Here's my setup for what it's worth. IMHO Q towers are realistically the easiest, least painful way to do it. Any possible paint damage can be remedied with a simple buffing and wax. and that only comes from grime settling under the pads (it DOES happen) but it'll take quite some time to do so which is why I remove my rack a couple times a year. Generally I find nothing underneath, but on occasion (after alot of winter highway driving say) you will get some grit, I've yet to have it do any damage. The clips do no damage whatsoever to your doorsills if installed right. just be very precise on the measurements they list and follow the instructions properly, or have someone who knows do it, you'll be fine.
http://www.msprotege.com/vbb225/showthread.php?t=82968&highlight=yakima
Feel free to ask me any yakima Q's I'm a certified Yakima RackDawg and have been installing them for 10years now.