I've exported some H.264 format footage using the YouTube 720p HD and YouTube 1080p HD presets and then uploaded these to YouTube and its created video with very minor letterboxing.
My original video footage was recorded using an old Sony VX2000 with the format set to 16:9 WIDE for long shots and a Samsung S7 Edge phone recording in 1080p for close ups, so possibly this is why i'm getting letterboxing, but it'd be brilliant if someone could confirm?
Something worth noting is that my A roll footage was from the Sony VX2000 and the B roll the Samsung S7 Edge. When I added B roll footage to my timeline I had to resize it using motion as it was massively zoomed in compared to the A roll video.
I'm going to use a digital SLR next time combined with the Samsung S7 edge both recording in 1080p for the long shots and close ups respectively so i'm hoping this will prevent the letterboxing from occurring.
If so, you are mixing 720x486 interlaced with 1920x1080 (also interlaced, I am guessing). If your timeline is based on the VX2000 footage, that would explain why your 1080 footage seems huge when brought into the timeline.
The above involves some guessing, of course.
If my guesses are correct, you have different resolutions and pixel aspect ratios. Your SD widescreen from the VX2000 will have rectangular pixels with an aspect of 1.21/1 (if memory serves). Your HD footage is square pixel, so 1/1.
Your presets assume youa re working with all HD footage, so you are getting slightly funky results. Since you are blowing up the SD footage to HD sizes, try working in an HD timeline, and making the SD footage fit. Then your uploads should happen without the slight letterboxing.
Again, the above suggestions involve some guessing about your footage and timeline.
Dell Precision T7600 (x2)
Win 7 64-bit
Adobe CC 2015.02 (as of 6/2016)
256GB SSD system drive
4 internal media drives RAID 5
Typically cutting short form from HD MP4 and P2 MXF.