The Ceremonial of Bishops (CB) supplies the missing rubric from the GIRM:
149 Next, the censerbearer goes to the bishop. As a deacon holds the incense boat, the bishop puts incense in the censer and blesses it. The bishop receives the censer from the deacon and, in the same way as at the beginning of Mass and accompanied by a deacon, incenses the gifts, as well as the altar and the cross. After this, all rise, and a deacon, standing at the side of the altar, incenses the bishop, who stands without the miter, then the concelebrants, then the people. Care should be taken that the invitation Pray, brethren and the prayer over the gifts do not begin until the incensation has been completed.
So all rise after the altar is incensed, and CB does not provide a rubric for the people (or anyone else) to sit after that point; so the congregation is standing when the bishop says “Pray, brethren…” (CB 151).