This line is meant to convey the fact that the three ovas follow directly after the original 12 episode series in terms of story. If the original Genshiken had been 15 episodes the three OVA's would have been the 13th, 14th, and 15th episodes (albeit with different animation).In each of the 3 DVD releases for that Kujiun series was an ep of the Genshiken OVA. These Genshiken OVA's were essentially Genshiken eps 13-15 .
The OVA's pick up the manga story from where Genshiken stops and Genshiken 2 picks it up from where the 3rd OVA left off. Not watching the OVA's would be like skipping episodes 13-15 of a 27 episode anime. Considering new characters are introduced and the plot advances you're missing out if you don't watch them.
In case you were planning to ask they were subbed by gg. gg's tracker has apparently kicked the bucket but I believe they are still on irc bots in #gg on rizon.
Genshiken, the Genshiken OVAs, and Genshiken 2 all represent a single continous story, the same story that is in the mange, except the manga doesn't end where Genshiken 2 ends.
The Kujiubiki Unbalance episodes released with the Genshiken S1 DVDs (which are NOT related directly to the 12 episode series) can be obtained either here by Anime-Faith and Digitalpanic or as part of the [LIME] Genshiken DVD batch which also includes all of Genshiken season 1.
The 12 ep series was subbed by some group called yu which has since fallen off the earth
Kujiun 01-03 - [yu]
Kujiun 04-06 - [yu]
Kujiun 07-09 - [yu]
I can't find torrents for eps 10-12.