Getting a new car always has a learning curve with regard to how things operate and where they are located. After 12 years with my previous car, there were quite a few things that I found annoying because of the differences in the the Pilot. Now, very few are still an issue. However, neither of the things mentioned above were ever a problem for me.
I confess that I don't use the door lock once the doors are closed, so it might be awkward then, but I do use it every time I exit the car and want to lock it. (I was used to doing this with my Jeep, it saves the battery in the remote -- slightly -- and it allows me to set the locks while a door is still open -- which is a PITA about the remote.) I can't say that I have ever found the use of the door switch to be anything but a breeze.
Likewise, the window operation has only given me pause when I have accidentally activated the Auto down feature when I only intended to lower the window a bit -- usually in the rain or snow. Since I never had an automatic function on my power windows I'm just not used to it, but I do like it! I have never hit the wrong button and opened the wrong window, though.
I guess this all just proves that I'm a bit odd...