Hey Graham,
Considering this is community Q&A rather than featurerequests@audiokinetic.com or some such email; I will try to give you my "2 cents" about why you might not really need FLAC here, as another user.
Consider that when syncing from source control data is either transferred ideally at 1Gbps on a local network connection or as fast as your line to the remote location. When this data transfer is done it will almost always first compress the data over the wire ( with p4 this is a compressed workspace ). While its true that FLAC would yield a slight improvement over generic compression ( DEFLATE etc. ) its probably not worth it.
Even if you do have a good case for not wanting to shift the generically compressed data over the network consider that most version control systems ( the exception here being git ) will let you place the files on disc where you want and then let you do an update on files that need to be changed ( with p4 this is $ p4 clean -w ). So this would let you use a USB3 or other high speed connection to copy them from another user at least initially.
Ok so maybe you decide that these alternatives may or may not work for you but what's the issue with FLAC anyway? The problem as I see it as really you are only optimizing for disc space by using the format, for the reasons listed above, at a cost of additional cpu overhead to decode the files notably during a soundbank build and that usually disc space is not really an issue. Indeed a $300 10TB hdd can hold around 8000 hours of stereo linear PCM.
There is another smaller reason that I generally do not like FLAC on disc for working files and that is that its slightly harder to write small tools ( or use existing ones ) that only work with the simpler RIFF/WAVE format files - this may or may not apply to you.
Do also double check that your original files are not needlessly at a higher sample rate or bit depth that is required. Consider that all files will be truncated to 16 bit and optionally dithered and that your soundbank conversion settings may mandate a resampling of your audio. Some of these conversions can be done ahead of time depending upon the future life of that file, potentially at a higher quality, and save you some file size. Needless to say I've seen plenty of people storing files at 96kHz/24bit and all that ever happens to the files is they are resampled and truncated to 48kHz/16bit. A better choice here would be to have your actual originals and the data set you have prepared optimally for wwise in seperate places so that if you do need that extra spectral data or bit depth you haven't lost it for good but you don't pay a daily price for that.
Another more out there solution - do you actually need this data to be in source control? Would it be sufficient to have a network share or similar containing all of these files and a simple script to rysnc them to a sound designer's Originals directory? "Source Control" could be just be a tar/rsync of the directory nightly or more often.