What can make it confusing is that there are changes in terminology across sutta/vinaya/abhidhamma/commentary. These changes are not necessarily inconsistencies, just progressions in terminology (e.g. the the five-jhana, rather then four-jhana, model, new terms, changes in meaning of terms, or new collections of phenomena). "The Buddha never said (exactly) that" isn't a useful yardstick of consistency either.
And, of course, the existence of various modern Dhamma models (e.g. around Dependent Origination) that differ from the Commentaries doesn't prove the latter wrong. That's a matter of preference rather than an inconsistency in the Commentaries.
It might be interesting to examine some of the claimed inconsistencies in detail, such as the ekagatta example:
http://dhammawheel.com/viewtopic.php?f= ... 09#p356131
and see if they are really inconsistencies
, or just changes in classification, etc.