Jason, this is a good question. The flow step doesn't specify which program, while the similar criteria in the smart list is more specific, so it is vague.
To make it easier to understand your campaign, I would design it to emphasize the smart list criteria:
1) Send email campaign: send email 1, change progression status to sent, wait six days, send email 2
2) Listen campaign: if email 1 is opened, change progression status in this program to "opened"(or similar) and remove from flow of campaign #1
This sets your first campaign as the default path: send both emails. The second campaign defines the criteria if the thing happens that you want to achieve.