is it ok to operate a boost converter with the input higher than setpoint?
It depends upon the converter.
For a common non-synchronous boost converter it is usually no problem.
When the input is above the set point the duty cycle will go to zero, regulation will be lost and the output current will be supplied through the pass diode.
I've used that approach with an LT1949 device that was fed from a battery to avoid brown-outs.
It looks like the LM2586S-ADJ would support that mode of operation.