The instrument is very stable so the neck should be nice and straight. Personally i never noticed any difference with the lower frets except for the fret right over the damper which even on my Grand Stick which takes a touch more energy to sound. If you feel the strings closer to the damper need more energy to sing one thing you may try is to raise the nut screws a quarter turn and see if that makes a difference. Just remember exactly how much you adjusted them so if it doesn't make you happy you can put them exactly where they were before the adjustment.
There's a learning curve, especially when you TWO hand tap. So take your time and get the know the instrument. The tuning may be comfortable to you but having an instrument set up for two hand tapping is a new world.
Enjoy your journey! And as always ... ask all the questions you have.