Regarding the Group B classification for higher education or skill training, the issue is between classifying a space as Group B or E. If 12th grade and below, then it is classified as a Group E. If for higher education (i.e., colleges and universities) and skill training, then they are classified as Group B. However, if the occupant load of a Group B education space is 50 or higher, then it is classified as a Group A-3 to address the issues of a higher, concentrated occupant load. Group E incorporates special life safety requirements that are lacking in Group B requirements; thus, there is an exception in the Group A section in Chapter 3 that does not require Group E to comply with Group A requirements.
As to the original question, I would say no, that not all occupants need access to all three exits. The floor will require three exits, so a third exit will need to be added, but if the area under consideration does not require three exits (i.e., the smaller tenant), then they only need access to two exits. The other, larger tenant, however, will need access to three exits, whether they share two with the other tenant or not.
Don't forget about egress width. The higher occupant load may require wider stairs; or, the new stair may need to be sized to accommodate the difference, as long as it does not provide more than 50% of the required egress width.