Answers
1. Yes , he let you in on your work permit, you can check this by seeing if he used a pen on your IM1 visa and struck through the visa, if he did that, then he let you in via the one time visa, but if the one time visa remains untouched with no pencil or pen marks then he let you in via your wp. Pretty sure at this point i can say its your wp and not the IM1 visa.
2. If you do it via international airport, they cannot deny your landing, regardless of when you arrive at the airport. So they will process your landing, this is probably the best way to complete landing, but those of us living in Canada have no intentions to fly out and come back just for this. But if you have a trip coming your way then it becomes easy, which seems to be your case.
2.1 Check my answer on point 1, there will be marks on your single entry visa if he let you in on that visa.
2.2 No they cannot, if you enter Canada by AIR, they have to process your landing , no choices here for them
2.3 Same answer as above
Additional information : There are two things, one is your work permit, which is not used as visa for cross country travel, so you must have had a temporary VISA to enter into Canada, if you did not have this VISA, then he would have let you in on the single entry, in such cases the only option you have is to book an appointment, as you do not have a temporary VISA to do another flag polling. So if you only have your work permit , and have already used your 1 time VISA, make sure you do not go out of the country , your only option is to book an appointment and wait for it.