Crafter SA and SAT models are supplied from the factory with electric strings which are used because the magnetic pickup responds the best to this type of string. Acoustic strings will not work properly with the magnetic pickup. Electric strings are not optimised for the acoustic under saddle pickup but the difference between the response to these and acoustic strings is negligible.
The gauges of the strings fitted at the factory are .011 to .049 and small changes to these gauges should not affect the intonation. However, if you use a set with a wound third string the intonation will almost certainly be out and you will need to change the bridge saddle. A suitable replacement is supplied with the guitar.