I never used the /3gb switch, but only /pae for Windows 2003 (32-bit Enterprise edition with up to 16GB memory assigned), and never had any issues with this. As you can see in the article you mentioned, the issue has already been resolved in a patch for version 4.1.
I'd say go for it. Btw. The lastest Converter versions offer an option to align the file system/partitions from 31.5kB (63 blocks) to 1MB (the default for newer operating systems).
André