How do I resolve inconsistencies between the rules committee Commander rules and the comprehensive rules?
How to Resolve Inconsistencies
First, try to determine whether there are actually any inconsitancies. For example, the mtgcommander.net forums have their very own thread discussing the matter of Devoid specifically. The most concise explanation seems to be the one from Carthain:

(...) Colour Identity is the culmination of colours + colours of mana symbols on the card. It's a purely additive situation, you can't &quot;lose&quot; or &quot;undo&quot; adding a colour to a card's colour identity.
Devoid says that a card is colourless. It it's a characteristic defining ability that sets a colour (colourless is not a colour); it's not any of the mana symbols that define a colour; it's not a colour indicator on the card; Therefore, it doesn't have any impact on the colour identity of the card.

Sheldon Menery writes:

Color and color identity are two different (but related) things. Colorless-ness is not part of either.

Therefore, Blisterpod is colorless and has a green color identity, according to both sets of rules.
This being only a single case, it raises the question whether one set of rules does generally take precedence over the other, and which one does. So...
Which Rules are the &quot;Official&quot; Rules?
In an effort to solve this question better than with a guess, I decided to take the time and write something up that explains the historical events as well as their implications as best as I'm able to. Because there's no set-in-stone answer to be found anywhere, I encourage you to read through all of it, even though I have my own conclusion all the way on the bottom.
The EDH Era
Without going too much into historical matters here, this article will tell you a whole lot about the history of the format. In any case, the format has existed under the name EDH long before WotC took it up as Commander, and dragonhighlander.net (now mtgcommander.net) is the original web page where the rules were first made available online in order to reach a greater audience.
This doesn't really help answering the question directly, however it disproves the first paragraph in CyberClaw's answer, which states that mtgcommander.net is meant merely as a &quot;short quick explanation without any kind of deep rule (or care on their wording).&quot;
The Commander Era
WotC eventually incorporated the format into their franchise by announcing the first Commander set along with the name change from EDH to Commander, and the respective WotC announcement mentions several important factors to the question at hand:

(...) we recognize the importance of keeping the format as player-run, even after we produce products that officially endorse it. To that end, we worked closely with Sheldon Menery and the rest of the EDH Rules Committee (we're lucky to have one of them, Scott Larabee, in house) to make sure our product adhered to their rules and stayed true to their spirit.

And further down in the article (emphasis theirs):

And finally ...
Wizards of the Coast and the DCI are not &quot;taking over&quot; the format! We will not be managing the rules or the banned list of the Commander format, instead leaving it in the capable hands of Sheldon Menery and his rules team. They deserve all the credit for this format's popularity and we don't want to mess with a good thing!


Conclusion &amp; Implications
WotC still considers the Commander Rules Commitee as the maintainers of the rules, as evidenced rather clearly in the aforementioned sources directly from WotC. I haven't been able to find any evidence disputing what was said in those articles, or a change of mind at a later point in time.
The Commander Rules Commitee is in charge of maintaining the rules and the ban list and therefore the technically official source for rules, while WotC is incorporating those rules into the CR in a way suiting the style of the rest of the document, and likely being more precise as a result of that, making the CR the source probably best suited to resolve rule questions.
They aren't meant to be functionally different though, and if there were differences, they would likely be mistakes and the Commander Rules Commitee rules would have to take precedence (which has happened before, as acknowledged in an announcement about former rule 903.4 about color identity).
Knowing all of the above, keep in mind that Commander is a social format - in the end, what your player group wants to play should decide which cards you're allowed to include in your deck, whether it's a Blisterpod in an otherwise colorless deck, or a Spell Counter (just maybe keep some alternative cards around, should you meet a group who does not like the idea).
This means that ultimately, your playgroup is the final authority on each and every rule.