It's one of those "it depends" things. Yes, changes you make to an existing port channel will be applied to all the links. But it's best to get them to match first and makes your life a little easier.
If you have timing issues, from one side to the next, you may end up with some links in err-disabled mode as you are initially setting up and building the etherchannel!
But those things should match in as much as you expect them to work! e.g. VTP really doesn't matter to the etherchannel, but if you'd like it to work it matters!