The in game teleporter system is very useful for getting around, however certain missions will lock out some destination options and you are unable to teleport while in a restricted zone. This is intended to prevent players from cheesing certain missions. Luckily we can get around this and indeed use the teleporters to cheese those missions though (at least as of the current patch, version 1.1.1). There are two ways of pulling this off, I'm going to address both.

The first and easier method is quite simple. Once you accept a mission the game takes a moment before it locks you out of teleporting. If you (on the PC) hit the F key to accept the mission and immediately hit the M key to bring up the teleporter screen, if you have the right timing the game will have not locked the teleporters yet. This timing is tight, however, we can solve for that as well. If you attempt this and fail, hit the cancel mission button and immediately repeat the previous step. Canceling this mission creates a slight amount of lag making it extremely easy to hit the now larger window to get this glitch. This glitch is extremely useful for the mission High Stakes, as (at least in the Any% run) we don't have banana flight yet. Instead of doing the mission normally you can run to the top of the building (without there being any guards) to activate the teleporter, then teleport back to where you accept the mission and use the glitch. This will allow you to teleport directly behind the target and avoid having to deal with any of his guards. This is also useful on the Wing man mission as its faster than either using bananas to fly to the roof of the cathedral or running up the stairs to get there.

The second method is harder to pull off, but is extremely useful for one mission in particular, Protocol 42. Protocol 42 has a cut scene that triggers as soon as you accept this mission that pulls you out of the normal in game engine. This prevents the first teleporter glitch method from working, as you will not be able to bring up the teleporter screen at all. Instead we need to do what is probably the closest to a frame perfect glitch this game has. The second method required you to be standing on the place where you would accept the mission and opening up the teleporter screen. Find where you want to teleport to, click the location and immediately hit the F key (not at the same time, right after). There is a fraction of a second between you choosing where you want to teleport to and you actually teleporting where you are still in your original position according to the game engine. If successful on the Protocol 42 mission you should see yourself teleport before the screen goes black and the cut scene starts. If you fail you will simply have teleported to your target and not triggered the mission. Luckly this trick saves you over a minute and takes very little time so you can easily teleport back to where the mission is started and try again if you fail. As a fun bonus if you succeed the ensuing cut scene glitches out and the ground is missing, which is kind of funny. Unfortunately this requires clearing the gang stronghold that covers the area, is not terribly useful for the Any% run unless you can clear the stronghold very quickly and pull of the glitch in a try or two.

Edit: Protocol 42 skip if done on the first try and with a pretty fast clear of the gang stronghold can save about 45 seconds give or take. I pulled it off once and it was glorious. This certainly is a viable strategy for Any%, but its still quite hard to pull off and starts losing you time if you fail 3 or 4 times.

Hope this helps any would be runners.

Edit: Here is a video showing the Protocol 42 skip which is the more difficult trick: