IANAL nor am I a Tax Advisor, but from my understanding transferring the shares for a value for obviously less than the fair market value would come under scrutiny because the tax authority could interpret this as a way of evading income taxes for the founders.
We've had a similar situation happening and it took quite some legal fees to ensure we had all answers ready and in writing before the tax authority would start to ask their questions. It's a complex situation.
Another sad thing is, you can easily get buried in the costs of Legal/Tax advisor costs even for some simple stuff.
That is why sometimes its better not to 'entreprendre' anything while living in Germany. The system is setup in a way to make you work full-time for corps.
We've had a similar situation happening and it took quite some legal fees to ensure we had all answers ready and in writing before the tax authority would start to ask their questions. It's a complex situation.