Your observation makes perfect sense.
Stern does not use a woofer in their games, instead they use a full range 8" speaker. This is producing some bass with a bunch of midrange and little treble. To get more and better bass, replacement systems (mine included) use a true woofer with a low-pass filter to get rid of anything but bass coming from this speaker. This is the reason some voice calls will reduce in volume. With the lack of full range 8", we must rely more on the back box speakers to take up the slack. In my systems these are running full range for this reason.
Here are some settings you can make to bring the voice calls back to the appropriate volume.
Under Feature Adjustments:
#39 Music Volume set to -20
#40 Speech Volume set to -25
Yes, these are negative numbers, they are backwards from conventional thinking.
This will bring them back to what we will call expected volume. Personally, I no longer use the l-pad supplied with the system. It is there for the owner that wants the most bass they can possibly have. Then I set the game volume at anywhere from 52-55 depending upon my mood. These with the settings above will yield a great user experience.
I am always available for questions. I will not post my number here, but it is at the end of all my installation instructions on my website under "Flipper U" and also now included on paper in my systems.