I've etched the boards and the clay on the traces caused no problems. Maybe it just adds an extra layer of resist. Over the years I have made probably 50+ boards, On the first ones when I was a young teenager the resist pattern was applied with a paint brush using model airplane dope, that was before the days of ICs or SMDs. The smallest footprint was a 1/2W resistor or TO5 transistor. Most though have been done with hand drawn art work photographed on litho film and used on boards sprayed with photoresist, and etched in ferric chloride. A number years ago I switched to copper chloride as the etchant, it is slightly slower than ferric chloride but has a number of advantages, not the least of which is it never wears out, hence no disposal problems.
I had heard about using laser printers for the resist pattern but didn't do any thing with it till the #100 issue of MEW came out with a detailed description of the process. It wasn't till a few years later that I got a laser printer and could try it. I had already been using ExpressPCB for other things so it was a logical extension. I have found it much easier and faster than the photoresist method (other than the clay problems), but I'm not sure how you could reliably transfer the pattern on a large board. (The largest I have ever made was 8" x 10" double sided. although I can't see myself ever having to do that again).