Because it is better for them (and for you) to do it twice.
The physical check-in is optional, now many people check-in online or at various electronic kiosks, so a check should be done at gate, there is no other place that company staff have all passengers.
But what happens if on check-in they give you a ticket and later you will be refused to board and all done by people of the same company? So it is good to have the visa checked also earlier, so that nobody could complain. And it reduce costs of retrieve an already sent baggage. (the first check is usually not only on check-in but also on baggage drop-in for automatic check-ins).
Airlines face heavy fines if they bring someone into a country without valid entry documents. Ryanair, a budget airline, operates with low profit margins as it is, and even a single fine can be really detrimental to their bottom line. On the other hand, doing an additional check costs them almost nothing. It also has the following benefits:
Credit:stackoverflow.com‘
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