Generall,y that would not happen and I have not use case where 2 bearers have same QCI. However yes it is possible, as in your case user is going to connect to 2 different APN so the sessions will be different and hence can have bearers with same QCI.
In case you are connected to only 1 APN, technically in that case also, you can have 2 bearers with same QCI because bearer binding is done by PGW based on QCI and ARP( Pl, PCI, PVI). So, if QCI is same and PL are different then also PGW can create 2 different bearers with same QCI.
Regards,
Peeyush Sharma