From what he told me about the company, they do collect/handle PII and
process credit card information. He also said, the company doesn't
have PCI or ISO 27001 cert nor are they looking at getting it done.
I suppose they are talking about the website, which is something completely different than the software they are selling. The company may also be processing credit card transactions through a processor, which means they may not have to fulfill all PCI requirements.
He even went as far as asking them if they do any secure code review
and secure coding practices for which they said they don't do any of
that.
At least the company is honest :) Perhaps try to engage with them and steer them in this direction if they are open to the idea ?
But you need to have this discussion with the right people, that is the developers and the technicians. Not the sales rep who is very likely clueless and unable to provide the qualified answers you are looking for.
My question is, did he go too far with these questions to the vendor?
I guess, when is it going overboard? Based on what the vendor said, is
this a bullet that his company is potentially dodging?
I don't think he went too far, he simply did not behave like an ordinary client. If you are going to install proprietary software on your machines it's perfectly legitimate to inquire about security.
There are things you can do on your end like containerize the application, although I am more familiar with Linux solutions than the Windows environment. You could even use virtual machines or intermediate solutions such as Docker. Perhaps you might even want to use a dedicated computer too.
Realistically, the application will probably require Internet access for updates, and even then you may restrict access to a few whitelisted IP address that the vendor should be able to provide. Assign a VLAN which is separate from the VLAN where the crown jewels are.
The application may also need access to a network drive for your blueprints or other work materials. So you create one, with the right ACLs. A supply chain attack is always possible but can be contained and limited.