Update on this as I've tried to transform my Matrix planning into a purchase on the ANA site. The ANA site appears to be using the fare rules that are listed in ExpertFlyer, not the fare rules that ITA Matrix is using. In particular, the website is offering me a routing with an AS leg that ITA Matrix refused to price. ANA is also enforcing a restriction whereby any surface sector creates a stopover. ITA is allowing a surface sector < 24 hours without triggering a HIP check, but ANA is not. In practice, that means that you can't, e.g., fly into Seattle, drive to Portland, and continue on to SFO from there. (No, I still haven't been able to figure out where ITA is getting its set of rules. I''ve tried messing around with the point of sale in both EF and ITA, and it doesn't seem to alter anything...)

Note that ANA uses married segment logic. If you want to fly, e.g., KUL-JFK, and you don't want a stopover in Tokyo, you need to search KUL-JFK inventory, not KUL-TYO and TYO-JFK. I ran into a case where KUL-NRT and NRT-LAX were both P2 but KUL-LAX was P0. ITA also missed this, somehow.

I'd be interested to hear any reports from people who have tried creative routings with an OTA -- do they ticket according to what you see in ITA Matrix or what you see in ExpertFlyer?