Which BAMT version do you prefer and why? Looks like the author of that FAQ advocates the unofficial 1.5.2 and 1.6.x based versions due to out of the box multi algo support.
I began using BAMT with 1.3, and then tried 1.4 and 1.5 when they were released. BAMT was slightly situational for these 3 versions - I ran exclusively R9 series AMD cards, and the best drivers for R9's are 13.22 which came pre-loaded on BAMT 1.3.. 1.4 and 1.5 were a mess for various reasons (issues with 1.5 out the box specifically changing the cgminer folder names in /miners/, and the terrible 14.x drivers they had installed were rubbish on R9 cards). Because of the drivers loaded onto 1.4 and 1.5 I was never able to match the hash rates I could get with 1.3, so I stuck with 1.3, and then the early vertminer 1.5 when I needed to mine Vertcoin.
Bajawah then did an unofficial release for 1.5.2 which I found to be superb. Well designed with the right SDK and 13.22 drivers for the R9 series, it was the first real upgrade for me since 1.3. The fact that it was easy to toggle between Scrypt and Scrypt-N with two lines in the bamt.conf file meant I no longer had to have two USB sticks per miner and no longer had to manually toggle them when I wanted to change - a huge bonus.
Then, Bajawah released 1.6.0 almost at the same time that the authors of 1.3 and 1.5 released 2.0.1. 2.0.1 is a hot mess of bugs for USB device booting, and still has the same problems with drivers that 1.4 and 1.5 did - making it pretty much useless to anyone running a R9 2xx card. Why they continue to develop for antiquated hardware is beyond me, but for all intents and purposes this means I shelved my 1.5.2 installs, ignored/skipped 2.0.1 completely, and started using 1.6 by Bajawah.
1.6 is friggen fantastic. All I really have to do is update the PoolManager to Starlilyth's most recent release and it's up and running. It allows you to toggle from scrypt, scrypt-n, and darkcoin with a simple edit in the bamt.conf, and has precompiles for a total of 4 different miners including support for rawintensity.
My two cents is Bajawah does a much better job at catering to the R9 crowd. 2.0.1 has the same problems that 1.5 did and more, and just like 1.5 they don't really seem interested in fixing those issues and updating their download, so the user has to do so.. irritating.