I agree this would be a useful feature for freshclam. If freshclam pulls down .cvd files to the PrivateMirrorís web server DocumentRoot then a client instance of freshclam with PrivateMirror set should try for those files first. They probably do .cld files first because .cld files are uncompressed and easier to work with (if they are available) but thatís just a guess.
At the very least, there should be a freshclam switch to choose to try one or the other extension first. Either way, if you want to see that changed youíll probably need to hit the developer list to inquire either how to submit a feature request (and wait however long that takes for it to happen) or see if anyone can guide you to where in the code that order is set and how to change it for your own custom build (which sounds like a lot of work to me).
Or you could do what I did and accept that this is how it is and filter the offending lines before they get sent upstream to the log aggregation server (if youíre not under some legal / regulatory obligation to retain all logs, untouched).
Best of luck!