When creating a connection to Adobe Analytics from your Funnel account you get to select up to three elements. Because of how Adobe Analytics works, the elements you select will affect the Visit based traffic metrics (ie Visits, Entries, Exits and Bounces).
1. Why the elements selected can affect the metric values
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 make sure you look at the correct data
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. Doing this will ensure that you always are looking at the correct values, no matter what dimension you are looking at or your account setup in Adobe.