1. Why Adobe Analytics metrics are non-aggregatable
For example a user could make a visit via tracking code 1, leave and then visit again via tracking code 2. Then if you include the Tracking Code element you would have 2 Visits, one for each, but you'd only have one Visit if you are looking at the data without the Tracking Code element.
Adobe defines Visits here:
Why Marketing Channels in Adobe Analytics increases Visits:
Why the elements selected don't always match with how Adobe calculate totals (using the Product element as an example):
2. How to work with non-aggregatable metrics
We would recommend you to create separate connections to Adobe Analytics depending on what you want to look at. If you for example want to be able to look at metrics per Country only, then you could create one connection containing only the Country element. Then if you know that you'll want to look at Tracking Code, Product and Country at the same time to make some analyses on that, you could create a separate connection with those three elements. You will not see any double counting since separate metrics will be created for each data source. You can the look at the metrics together with their respective dimensions in Funnel or wherever you export it.