Yes, if you change your font then the font of clockr will change also.
Edit: It just came to me. With temp root (I could be wrong) once you reboot you lose root, right?
If that is the case then you won't be able to change your font. When changing your font the phone has to reboot when using the app from the market. Never went to the file with the font to change it from there but I would assume that you would still have to reboot anyways.
From what I mention first, you can change the font of clockr but looks like you need full root instead