The PRESUMPTIVE LOAD-BEARING VALUES table in the IBC is meant to be used with ASD loads (see section 1806.1). As such there are already factors of safety "built in" to those values. The only thing I am aware of that the IBC has to say specifically about shallow foundation settlement limitations is in section 1808 (not even worth quoting).
The values in this table have been inherited from a number of sources, including the Uniform Building Code (UBC) and the BOCA, which have tables with very similar numbers. The commentary for the UBC (1991 edition) indicates that the values are based on:
- a factor of safety against general bearing capacity failure of 3.0, and
- a total allowable settlement of no more than 0.5 inches.
Settlement and allowable bearing capacity, although related, are different conversations.
The industry standard factor of safety used for allowable bearing capacity for a very long time has been in the range of 2.5 to 3.0 (depending on the type of data that is available), so the table is on the higher end as one would expect.
Typically, settlement is often the governing design criteria and the typical allowable settlement limit is considered to be on the order of 1 inch to 2 inches, with a differential settlement limit of about half of that. So again, at 0.5 inches it appears that the values in the table seem to be on the higher end of the safety range as one would expect.