If there is a question regarding the accuracy of the displayed RSSI value, you can typically compare the RSSI or RSL to the expected RSL for a given MSE by checking against the published receive sensitivity on the datasheet and the maximum MSE allowed for a given modulation.
For example, if I'm running a 56 or 80 MHz wide channel, I would expect the RSL to be about -65.8 when the MSE is -28. Typically by lowering the transmit power I can reduce the RSL to get it close to -66. If the MSE is worse than expected when the RSL is -66, then I can assume that either the RSSI display is not correct (in the case of older hardware which has to be calibrated for RSSI display) or that the alignment is off in which case the signal will be distorted more than expected based on the given RSL.
For older SP ODUs and Apex that relied on a calibration, the hardware must come back to the factory for proper evaluation.
For newer HP ODUs, the typical cause of poorer than expected MSE is either alignment or a cable issue. If the RSL is symmetrically low on both sides, it is almost certainly an alignment issue.