Correct me if I am wrong but I think according to "30 minute backlinks" (and you referred to it) you have to link to a direct download page on your site. If this is true you can't choose what page the backlink points to.
If you review the 30 minute backlinks package more closely then you will find that the you can choose where the backlinks point to. That choice is further limited to your homepage because you must upload a "downloadable" file to your home directory that the software sites can verify.
So, in the end you can choose where you point the backlinks to but they will be limited to the homepage of your site. In other words, using this method of backlinking is limited strictly to your homepage or commonly known as "shallow links".
You CANNOT "deep link" to your internal pages.
You said people download from the software directories. The author of 30 minute backlinks said people download from your site. Could you please clarify because I never used the software method before. Thanks
You first create your "software" on your own using progz like GSA softsubmitter (paid, supposedly the best in the market) and you submit prog with the .pad file. So, to answer your question you are hosting a .pad and .exe file from your server and then you upload to the software directory. when your software is posted, you get a link to your site via the "download" link...
Backlink created via the download page on a site like "freedownloads.c0m" and many other sites that pick your .pad.
You host the file, directories pick it up and link to your homepage/home directory because you have no choice. Make sense? Good, now I'm not sure if it works anymore is the caveat...many directories have picked up on this abuse and GSA softsubmit is really advanced but also really regulated on if you are going to submit bullshit like toolbars from conduit for example.
IMHO expect less than 50% success rate on posting and even less on backlink acquisition. However, since you can throw this all together and get 200+ backlinks with about 30mins work then you must reconsider on your own personal level of input v.s. output. have fun!