Will using a dimmer switch damage a transformer?
If they say they are not for use with a dimmer they mean it. Regardless if you set it at 50% and leave it or whatever. Yes, you will damage the transformers or electronics of the systems if you use them on an incompatible dimmer. 

Don't forget, many low-voltage lighting systems can be used with magnetic or electronic low-voltage dimmers. You need to check the manufacturer's specs to be sure.

Lutron, a leader in dimmer technology, has a good explanation here: http://www.lutron.com/en-US/Education-Training/Pages/LCE/DimmingBasics.aspx