.. This statement is interesting.
A lot of the e-commerce software you can get for free is written in common web development languages, e.g. Perl/PHP/Ruby/ASP.
So is this a question of lacking in-house competence from a SMB perspective? Most OSS e-commerce packages I've used have been a breeze to install, never mind to customize.
The truth to the statement is that some things are, at best, poorly documented. But if worst comes to worst, track down the bit of script you need to know (how it works) and read the code?