What we ultimately care about is the net efficiency of the firm. Does the elimination of internal transaction costs outweigh the other inefficiencies the author points out? Internal economic exchanges as explicit transaction costs don't exist within the firm (e.g. acct dept does not send an invoice to the CTO for CPA work relating to budgeting the capital purchases of rack servers. And IT does not charge acct dept for upgrading the desktops web browser from IE6 to IE9.)
To prove the author's idea, the comparison would be something like:
A firm of 100 employees with those 19 inefficiencies underperforms and is less profitable than a loose confederation of 100 freelancers with their particular inefficiencies. (The 100 freelancers would also have a unique list of inefficiencies -- because nothing is perfect.)
We could also itemize 20 "inefficiencies" of the biological family unit. E.g. the child learns the language of his parents -- maybe Portugese -- instead of learning the most marketable and global language such as Chinese or English. The child eats some meals from grandmother's recipes instead of eating a scientifically designed diet for peak growth. And so on. Does such a list of inefficiencies convince society that Plato's idea of taking all children from parents and assigning them government custody is a better idea? That's the type of logic I see in the article.