Is it OK to have a PhD thesis with shortcomings and inaccuracies?
The thesis is a "good" one if you have passed and will be awarded your degree. Don't overthink it. You have learned something from producing it that you can leverage into future work. That is, in lots of ways, a big advantage. If your advisor is also happy and wants to work with you on any future extension, you have a positive outcome, if not a perfect one. 

That the thesis "might have been better, if only..." is true pretty frequently. 

My suggestion is to take the advice of the reviewers and get done. Then write a future paper extending and improving on the thesis. Don't make it harder than it needs to be. Your dissertation shouldn't be thought of as your life's best work, only its first. 

Don't let the perfect be the enemy of the good. (apologies to Voltaire)