The founders also could've created a UG (mini-GmbH), plenty of startups do. It's no clear from the blog post why they do the real GmbH. Possibly because a mini-GmbH can't be owned by 3 personal companies. Well, sure, in that case you need those 25000 Euro on the bank account.
Transparenzregister (transparency registry) was new in 2021. The notary should've done that step. Germany kind of added the registry so people can't hide behind personal companies when doing business.
Chamber of Commerce for an IT company is weird indeed. Makes sense for businesses that need special permissions, certifications or have regional limits (let's say pharmacies) but not IT.
Think of Gewerbeamt as local taxes vs federal taxes. Gewerbeamt is your city taxes. While federal tax rate is the same everywhere, city tax rate differs and allows them to compete a bit.
"so we had to agree with our investors that we would transfer the remaining 12,500€ over the next couple of years." Strange to have investors and then not have them pay the full amount. They're saving money here, true, but then shouldn't complain that this part of the process is not straight-forward.
Using a tax accountant for a GmbH company is not required. The author doesn't seem to grasp even the function of some of the contracts he signed so he should of course use a professional to file the annual accounts forms.
If you have money from investors and skip many of the steps: buy a holding company, costs 5000 Euro. You pay 30000 Euro and receive a ready-for-you company with bank account of 25000 Euro. Then go to a notary and have, in a single document, change the company name, change the shareholders, move it to the desired city.