Ok so I think this is all figured out. This problem is well summarized in this thread full of users caught in this scenario. Reading through the comments it becomes clear the user experience that leads to this confusion.
Essentially a normal non-tax-expert user doesn't know the ramifications of summarizing transactions and there is no warning in TurboTax until after e-filing, so people like me and many others that posted in that thread get bit with this. For example, in my case, my TXF import was over the TurboTax import limit so my accounting software summarized the transactions. This is all fine, but the problem is that there is no warning in the software until after you e-file. This means even if you manage to get a working itemized import (splitting imports up) you would need to amend your return!! This is complained about plenty in the above linked thread by several users and seems to be a general "gotcha" that I've also fallen victim too as well. I think Intuit forgets that most people using their software are not tax professionals.
