Why? If your airport is a small one that does not yet have baggage handling, why can’t I use the self check in desks? To my mind, there is nothing about self check in that intrinsically needs a baggage handling system.
Not everything ingame follows realistic rules. Otherwise, where is the web/app check-in? 
The automated check-in desks can be more compared with the machines to print the baggage tags.
For the time having no baggage system at all, the small check-in desks are supposed to be used.
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you can research baggage and use the auto stands and just not activate baggage handling.
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