Yeah that's correct, it mostly uses 32k cluster size and no games lag for me since I used this software for formatting, no 64k needed here.
OK. There may be a certain interaction with different cards. I just went though some testing with my Lexar 32GB and can confirm that I experience significant slowdowns when formatting the card with the tool you linked, compared to formatting with either, EaseUS Partition Master or with the Windows XP format command, but setting the cluster size to 64K. I guess each of us should stick with what works him, but the OP should give both a try, just in case.
I did my tests with Eternal Darkness and F-Zero, because those were the first games where I experienced my first slow-downs, even before reading this. In ED, with 64K clusters my only slowdown is while the Nintendo logo is coming up at the beginning. Coincidentally, the logo goes by just fine with 32KB, but then the Silicon Knights logo stutters, which does not happen at all with 64K.
The most dramatic example was F-Zero GX, when clicking on a cup to access the tracks in Practice mode. With the real disc, it takes about 2 seconds to access the tracks in a cup. With 64K, it takes about 2.5-3 seconds, but with 32K, it takes up to 5 seconds and the menu music always stutters. This stutter happens sometimes with the real disc, but with DML and 64K, I haven't had it happen.