TL;DR, Give Bob his money back.
Warning: this post does not hold back any punches.
This start-up sounds heinously predatory.
You are working full-time for just 500€/mo or 3.12€/hour?!?!
They're essentially trying to raise another $2,500 in seed capital from you by offering a stake in the company via loan and it's just a round-a-bout way of not paying you. If they're too broke to pay 3.12€/hour then that's a big red flag.
You've already agreed to the miniscule wage so you could certainly finish your internship since the programming experience should be worthwhile.
the start-up has raised 100,000€ of seed capital
This is effectively nothing. The start-up has conned 100,000€ from various people; 102,500€ if you accept the deal.
the software I'm working on would definitely give it an edge
I doubt it; a coffee costs more than your hourly rate. They've bolstered your confidence so that you're willing to make silly deals with them.
Lastly, from your linked post:
I have to build a complex multi-site web parser and a sibling web application (front-end and back-end) that exposes the parsed data to an an internal sales department.
Yeah, this is nothing new and is possibly against the ToS of the web sites they wish to scrape data from. If their business model relies on harvesting other site's/people's data then they really don't have a worthwhile business.