I “think” you will get +5V at the pin marked USB if you power it with 5V via the USB jack.
This is correct, see the pinout section of Adafruit’s guide for more information. You won’t get 5V if you power it with 3v3: there is a regulator which will step 5V from the USB down to 3v3, but it doesn’t boost 3v3 up to 5V.
The signal voltage will indeed be 3v3 but that’s actually almost always enough to drive Neopixels anyway. Strictly speaking Neopixels will run on 3v3 power too, just a little dimmer, but don’t try to power them from the 3v3 pin on the Trinket: the converter which supplies the 3v3 only puts out about 500mA, which isn’t enough for 16 Neopixels at full whack. Power them from the USB pin.
Assuming that you’re using CircuitPython to run them, check Adafruit’s Circuitpython Neopixel guide page. Just be aware that the Trinket M0 doesn’t have as much storage space as some of the boards, so rather than installing the whole library bundle you may just need to copy over the files you’ll actually use.