In "Tokenized Agent Setup Guide", someone gets an SHC share without paying anything

So the example in “Tokenized Agent Setup Guide” seems to be what I need for having a Reputation system where someone can be “granted” some reputation points without having to pay anything.

A level up from that would be a Utility Token where some payment would be involved.

And a further level up would be a Security Token where a payment is involved and the Security Token will be traded for speculative profit on an Exchange.

As I understand it, to turn that into a Utility or Security Token scenario (where you have to pay some money) there would have to be an atomic swap.

correct. For most share issuances/purchases there will likely be much more than just an atomic swap…like other types of agreements necessary to support the transaction.