If you have 3.3V only you should be able to power in via the 3.3V pin, say if you have a battery+boost circuit and don't want to have the onboard reg wasting power. You do have to be really careful that you can't exceed 3.3V if you do that though. The simpler design is to provide 5V to vin and let the regulator do it's thing if you already have 3.7-5.5V available in your design though.
looking at
https://www.pjrc.com/teensy/schematic.html the only thing the Vin does is power the slave USB port on the 3.6, so that won't magically get 5V if only 3.3V is powering the board.
Just wanted to expand a little bit on GremlinWrangler's response:
On Teensy 3.5 and 3.6 the incoming USB +5v power goes directly to pin Vusb, then through a cut pad to pin Vin, then through a fuse to the LP38691 voltage regulator that supplies the rest of the board. The LP38691 accepts 2.7v - 10v input, so the easiest (best under most circumstances) way to power the teensy from a separate regulated power supply is to cut the trace between the cut pads and supply your input power to pin Vin. This isolates the USB power line and pin Vusb from the rest of the board, and still allows you to feed the teensy with power through the normal path.
You can feed Vin with 3.3 volts if you wish. However, if you feed Vin with less than 5 volts, you will have less than 5 volts on the V+ line of the secondary USB port, and if you feed Vin with less than about 4.2v you will power the Teensy with less than 3.3v (dropout voltage of the LP3869x is listed as 500 mV @ 500 mA, but I measured a voltage drop of about .9V on my bench with only the Teensy as a load, so an order of magnitude off from the datasheet). The purpose of the secondary USB port is to let the Teensy serve as a USB host, rather than the way it is typically used, as a USB slave. I haven't seen many people using it this way so far, and unless you need it in your design, I would ignore that aspect of any voltage limitation. The Teensy will run with much less than 3.3 volts, but it's technically a form of overclocking so you have to know what you're doing.
Now turning to the issue of whether it is OK to feed the teensy power through the pin marked 3.3v. The answer is once again that you can get away with it if you really know what you are doing, but there are a number of downsides to doing so.
Power from Vusb / Vin goes through a fuse, ferrite bead, polarity protection diode, input filtering capacitor, voltage regulator, output filtering / loop stabilizing capacitor, and THEN to the 3.3v pin and the teensy power rail. If you supply your power directly to the 3.3v pin, you will bypass all of that protection and filtering, and your power will go directly to the chips.
As GremlinWrangler points out, the only advantage would be that you avoid the slight power cost of the LP38691 regulator (and the heat associated with it).
The disadvantage would be that all the chips on your teensy board will be dependent on whatever filtering and protection your separate supply can provide, plus whatever else you add into your circuit design. If your PSU has ripple and switching spikes on the output, that may cause gremlins to appear in your device. Or if another board being powered from the same supply creates voltage spikes/sags/digital noise on the power rail, all that stuff is going directly into the chips on the teensy. For example, if you power a motor driver board from your external supply, you'll very likely see problems if you feed the teensy with that same contaminated power and no voltage regulation / filtering. There's a reason that commercial electronics devices contain multiple voltage regulators, each dedicated to a specific part of the system and tailored to a specific set of requirements. Analog Devices has some examples showing as many as 20 voltage regulators in a single device.
I should point out that the power routing described above applies only to the Teensy 3.5 and 3.6, whose power routing is a significant improvement over the same routing on the teensy 3.2 board. On the 3.2, power comes from the USB +5 volt line through the fuse before it gets to the Vusb pin and a capacitor to ground. Then it goes through a cut pad to the regulator and the Vin pin.
The old 3.2 routing turned out to be a sneaky problem for me because I wanted to take some power from the Vusb pin. That pin came *after* the fuse, and the fuse has a resistance of 0.3 ohms. The resulting voltage drop put the voltage outside the USB specification range, so my (USB compliant) device shut it down right away. Also, there was no polarity protection on the 3.2 boards, and supplying power from Vin bypassed the fuse. I modified several of the 3.2 boards to get around these issues, and it's very nice to have it sorted properly on the 3.5 and 3.6 boards!!
