I was in contact with tech support regarding this when my greenphone was new.

When calling, the sound is routed directly to the GSM modem. Therefore, the way to adjust the volume is to use modem AT commands.
The following response was sent to me from Trolltech support:
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The microphone and earpiece speakers in the Greenphone are directly
connected to the modem(BCM2121), The audio signal is not routed through
the audio chip when on a voice call. The audio signal is routed through
the audio chip during a handsfree voice call or a headset voice call or
recording though.

You can modify the gain of the microphone in the modem, by sending an AT
Command to the modem:

"AT+VGT=X(X:0-9)"

0 is a special setting case. I am not sure at this time what setting we
set, if any. Please note that I have noticed some confusion regarding
these settings, that I would like point out to you.

In the above example, the range of X is quoted as [0-9], but I have
noticed some instances where [0-255] is suggested, with anything under
125 being a reduction in gain and anything above 125 being an increase
in gain. Fell free to try out both ranges, and let me know what worked
for you.
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I did not try it, since I had other building problems as well and did not have enough time then.
Today, my Nokia 6100 keypad stopped working, so I thought I should try to upgrade to 4.3 and see if the build problems were gone in the new open source version. However, I found no instructions on how to download the contents of the qtopia-greenphone-full-flash-4.3.2-no-sxe archive to the phone, so I guess I will have to compile it from scratch. Unfortunately they haven't solved my problem yet.

Let me know if you succeed with the AT commands. I will also give it a try after I have managed to compile 4.3, but since I now have a 1-year-old kid my computer time is limited.