If we select LTE and BLE antennas with lower gains than the reference antennas will our design still be certified?
You should consult an certification expert on this as the rules are complex, and vary by country or region.
In the United States, if the antennas are of the same type and equal or lesser gain in all bands, then you may be able to obtain a permissive change. You still need to request the permissive change to intentional radiator certification with the FCC - it's not automatic.
And you will likely also need to complete unintentional radiator certification of your completed assembly, regardless of antenna. This is the least expensive and easiest to obtain, however.