Needless to say, I think you can take their cryptic recommendations with a huge grain of salt.
https://twitter.com/matthew_d_green/status/47199831543788339...
The knee jerk reaction here is "omg, prism, Microsoft!". But the reality is that you have no idea who the TrueCrypt people are and their level of trustworthiness --- for all you know they work for NSA or FSB!
If you are a windows user, use the manual and use BitLocker for FDE and EFS for folder and files.
You can have the same assumption for BitLocker.
You wouldn't trust the drunk driver who's crashed his last few vehicles to borrow your car. The intelligence agencies own Microsoft, as far as users are concerned, and when cryptosystems have to be crippled for their priorities, we can't expect them to hold up to other attacks.
And for MS there is this story: http://www.geekwire.com/2013/report-microsoft-nsa/
This is of course no evidence for the (in)security of TC/Bitlocker, but I would call it indirect evidence, and certainly more than 'blind faith'.
So as far as I understand, it is possible to audit Microsoft's crypto code too. I can imagine the audit of crypto code wouldn't find anything. The real problem is:
http://regmedia.co.uk/2014/05/16/0955_peter_gutmann.pdf
"Crypto won't save you either"
"Crypto Summary:
Number of attacks that broke the crypto: 0
Number of attacks that bypassed the crypto: All the rest
- No matter how strong the crypto was, or how large the keys were, the attackers walked around it"
The fact the German and recently Chinese governments have specifically banned their users from trusting windows 8 + TPM doesn't thrill me with confidence.
The fact that bitlocker kindly sends a copy of your HDD recovery key to Microsoft if you have windows 8 linked to your live account doesn't strike me as brilliant, either.
Oh, and the fact I need to upgrade to the Ultimate or Enterprise editions of Windows means it doesn't help a large majority of users.
Even if truecrypt were written as part of an NSA/FBI joint project it's still works across the three main OS's and it has the source code available for scrutiny (deterministic build issues aside).
BitLocker is somewhat more business oriented -- thus they feature things like key recovery, more protection (or might be taken as limitation to some) when the hard drive is removed from one computer and ported to another machine, etc.
TrueCrypt seemed to be aimed more toward security than manageability, lacked those features above, which might have aligned with user demographies that these "business" requirements either they didn't want to have or not relevant.