Yep, good point, but I think It would be simplier to use the same feature if you're a pilot or not.
First, it might be a good idea to explain what are height and altitude to other users => height has the ground level for reference (AGL-above ground level). Altitude has the main sea level for reference (MSL)
There are in my opinion two options regarding aeronautical weather data :
-Forecaster point of view: Using charts, he gives the ALTITUDE of clouds (from MSL - main sea level) and doesn't care how you use the info...
-Pilots or controllers point of view: They don't want you to crash and provide the HEIGHT (from AGL - above ground level) of cloud base. So you have an idea of what you're going to see (or not...) while arriving or departing from an airport, whatever the altitude of the airfield.
Considering this, I think that giving the HEIGHT of cloud base is the best option (AGL), which is already the case. It is also good for non pilot users as it provides a useful and easily understandable info.
Regarding Freezing level... It's indeed more useful for pilots when using ALTITUDE (MSL) for other technical reasons. And... It's more logical for pilots but also for other users ... For hikers for exemple. They want to know the freezing ALTITUDE and not height, so they can compare it with the ALTITUDE of a mountain for exemple, because what is depicted on topo charts are ALTITUDEs.
A good solution in my opinion would be to use the words "height" and "altitude"in windy layers names and provide a clear definition of these 2 terms in the help forum section/legend, and obviously use MSL for freezing level and AGL for cloud base.