For your first part, I have also heard here in the forum that separately stated connection costs would not be subject to real estate transfer tax. In our case, it was also stated separately, but we paid real estate transfer tax on the full amount. I researched this about 4 years ago, but did not find anything to the contrary. However, maybe there has been some ruling or an administrative instruction on this in the meantime.
Regarding the second part, I would say you were lucky or the notary was not informed at the time of the second due date. To my knowledge, the notary passes the information on to the tax office. To what extent the company would also have had an obligation to inform the tax office about the change in the assessment basis, I am not sure. However, this does not change the fact that, in my opinion, the full amount would have been taxable.