If you're concerned about WAV vs. FLAC you should be concerned about the CPU first cause that is going to have more of an affect.
Yes, agreed, the whole computer thingy, my opinion, comes under the heading of a modern day miracle. And in my case, FWIW, these issues were already addressed in the system at the time of it's assembly. Win7, x64, AMD quad core, 8 gig memory, all on an ASUS MoBo with an ASUS STX sound card attached using an upgraded modular power supply unit supported by four HDD's for system software, media storage and back-up purposes via Norton "Ghost." By ripping WAV, there's no compression to deal with such as is the case with FLAC and my opinion, with the HDD's being both so big and so cheap, there's no need to compress music files; keeping it simple.
There's nothing the end users can do about the above other than to purchase matched parts from notable companies. In the case of music and music files, my opinion, it then comes down to keeping it as simple as one can. By needlessly adding more music related software, you're needlessly adding more processing of the music file. Not being a software developer, my understanding is to go with proprietary software as the insiders know their products and optimize their products to their products and the other products their products support as opposed to outside vendor, third party software adding another software layer.
Microsoft, ASUS and AMD (or Intel) are all in bed with each other as complimentary manufactures. Once you step outside this trinity, you're asking for software problems. Memory, same thing, name brand and matched sticks. Go with name brand product line as they have the resources to test to the many different possibilities for conflict issues. Again, doing it this way keeps product manufactures and software close to the vest regarding compatibility and conflict issues and keeps possible unknown conflicts to a minimum.
Same thing for the Blu-ray burner. The Blu-ray burner is a Pioneer unit, a company with many decades worth of experience and the money for product development. The point if you will, yes, the CPU issues were taken into consideration, long before the first music file was loaded onto the HDD.
In the end, there's only so much end users can do. After which, once the system is assembled, my mantre, keep it as simple as possible so as to keep those software conflicts to a minimum as software conflicts are cumulative. What's my idea of keeping it simple? No extra software and it's okay to use an EQ.