Is there a filter-reminder thermostat that uses run-time instead of total time?
Some programmable thermostats do base their filter reminder on run time.  However, the problem is looking at a filter, their change out period is not mentioned in runtime, it just says 'every 6 months' or something like that, so it's a little tricky to convert sometimes.
The Radiothermostat 3M-50 (in your link) says:

FILTER - AIR FILTER ALERT - The  3M-50 can be programmed to remind you
when the HVAC  sytem’s air filter needs changing. Touch FILTER. The
display will show the usage to Touch FILTER for over 3 seconds and the
display will change to LIMIT. Touch arrows to set desired usage limit
before filter alert comes on home screen.  When this limit is reached,
FILTER will be on home screen and the CHECK FILTER indicator lights.
Limit may be set from 0 to 999 days/99 weeks; default is 90 days/12
weeks. Touch to reset. To reset the usage back to 0, touch usage
number

However, I recently installed a Trane Z-Wave thermostat  and its filter reminder is based on hours.  As a bonus, you can implement Z-wave in your house!

The Filter Service screen will show the accumulated Filter Runtime hours as well as the Service Interval that will be used to trigger a filter message.  Any type of HVAC operation that causes the HVAC system fan to run will cause the Filter Runtime value to increase.