When my co-founder and I were creating our project (with a scientific background), we always listed our universities as our affiliation, or we listed ourselves as the Co-Founders of the project with an e-mail. For the last two years or so, my co-founder has worked at a technology company in the UK, while I am still on my PhD in the US.
Now, if we author a paper, is it okay to list my university and his work affiliation (the company)? Formally, this would be correct. However, he does not work on our stuff during work hours but only in his freetime and at home.
If we do list the two affiliations (university me, company him), does it imply that the paper has a commercial touch? His employer is okay with it.
Would this setup complicate creating a startup from now on?