This topic is always misunderstood, and no, its not clear as mud; it's just clear.
You need to come to an understanding regarding that last leg, however. Simply because the flight is operated under Part 91 doesn't mean it isn't being performed as a duty to the company. If the certificate holder assigns you to make the flight, you're still acting with a duty for the company, and whether you act under the operating regulations of part 91 or 135 isn't relevant. Who's being charged for the flight isn't particularly relevant, either.
You appear to be asking a question regarding the proverbial "tail end ferry." This occurs when your duty to act for the company has been completed, and you are free to act on your own. You are released. The company isn't asking you to make the flight. You may be out of duty time. You may have reached your flight time limits. However, you're stuck in timbucktoo and want to get home...the crew can elect to make the flight. The company can't ask the crew to make the flight, because that then becomes duty...something the company can't assign and the crew can't accept.
Once the duty to act on behalf of the company has ended, you're not beholden to the flight time restrictions, nor to the duty limitations of Part 135. In other words, let's say you have a crew of two and a ten hour flight time limitation. You are a regularly scheduled crew with a 14 hour duty limitation. You have reached 2200 hours at the end of your 14 hours of duty, and you've flown exactly ten hours in a mixture of Part 135 and Part 91 legs for your employer. You now need to reposition the airplane home.
The company can't ask you to do it. The certificate holder may not assign you to more duty nor to more flight time, and even if they do, you can't accept such an assignment. However, you can volunteer to make the flight (and this is an important technicality). Let's say you have a two hour flight to get home, meaning you will end up having flown 12 hours all told in the previous 24. Those two hour are done after your duty to the company has ended. They'll count against future flying (because it is commercial flying), but not against your past flying...duty's over, so this flying doesn't apply to the duty which has already ended.
This also doesn't mean you need sixteen hours of rest...becuase this isn't an operation assigned by the certificate holder. Your rest doesn't begin until you get home, but you don't need additional rest, either.
Now, change that a little. Let's say you're a regularly scheduled crew with a 14 hour duty day, and you've flown 10 hours by the time you hit hour twelve of your duty. You have two more hours of duty, and the company needs the airplane home. You make the flight, which lasts 60 minutes...and now you need sixteen hours of rest following the completion of the flight.
In all cases, the single biggest overriding regulatory issue, and the one which will be universally invoked during enforcement procedings if you do get yourself in trouble, will be 14 CFR 91.13. It's invoked in every single legal interpretation on the subject, and included in every legal action taken against a certificate holder or flight crewmember where rest requirements are compromised. 91.13 is, of course, careless and reckless operation, and you'll find that thrown at you in a heartbeat even if you're legal, if an inspector believes you've flown unsafely, tired, or pushed reasonable limits.
Just to muddy the waters a little more, my opinion is that the pax only pay for the leg they fly.
No water muddied there, because it's not relevant. You're getting paid to make the flight, and therefore you've engaged in commercial flying (which can still apply even if you don't get paid, but log the time...subject of another discussion for another time). It's commercial flying, regardless of whether the customer paid for the leg or not.
Why then would a reposition leg be considered as "paid for" by a customer since they could care less where you go next, or where you are coming from?
Again, irrelevant, because YOU'RE getting paid. It's commercial flight time. However, regardless of whether a customer pays for a leg or not, this doesn't change the ability to operate under Part 91 when no persons or property are carried between point A and B for compensation or hire. A tail end ferry without the passenger or his posessions on board can be very easily performed under Part 91, regardless of whether the customer pays for that leg or not...because who is paying isn't relevant to the question of duty or the regulation under which the flight is operated.
Simply because you make a flight on behalf of a client doesn't make it a 135 flight.
My only question was if 91 commercial flying is included in the lookback to determine if 16 HR rest is required if you have flown 11+ hrs., however you got there.
Depends. If that 91 commercial flying was done by assignment of the certificate holder, then yes it is included in the lookback and does determine the prospective rest to follow the duty and flight operation.
If that 91 commercial flying was performed after your duty to act for the company had ended, then no, it's not part of the lookback (but does apply looking "forward," in that it applies to your next look back cycle)...and doesn't increase your prospective post-duty rest cycle.