Custom only indicates that you've changed the preset in some way. In this case, by going from NTSC to PAL. It's fine to proceed from there.
The YouTube preset by default is set to NTSC as they have a standard set at 60i. I'm in PAL as well and found this.
Custom as Jim says just states that you have changed the preset...
Use a preset as a base.... Then make your specific adjustments to that and save THAT to your own preset...
Hope this helps
As soon a you change one parameter it jumps to custom.
Yes i am in pal-land too and its a bit of pita but set it to your liking (set framerate to 25) and make it into a preset.
You can also use one of the HDTV presets, then you do not have to set the parameters, you will be ready to go.