Hello, and welcome to the forum.
I am not sure what the three different frequencies that you list represent, and how these frequencies are actually measured, and over what measurement period. Keep in mind that, when the FLL is utilised, its output will have a substantial amount of short term jitter, as is the nature of FLL operation. As the time period over which the frequency measurement occurs is increased, the amount of jitter will steadily reduce.
The small frequency variations that you indicated should not be a problem for the MCU. The potential variation of reference oscillator frequency, with change of operating temperature, is likely to be considerably greater.
If slightly exceeding the specified upper bus frequency limit is of concern, you might consider a reduced trim frequency for the internal reference.
Regards,
Mac