Of course, the finally used audio format (e.g. WMA) doesn't matter. The challenge is to come to the pcm audio data as error-free as possible.
I guess you are planning to convert your files 'on the fly'.
In the case of these heavily hardware-dependent audio protections, you should be pleased if you are able to copy your CD to HDD uncompressed, at all.
So first create an image of your disc, and then convert it.
Just a hint: Why not check Upp3rd0G's sticky thread? It's worth it