It will work fine in speaker mode, because it uses a different microphone, speaker mode uses your microphone that is attached to the camera flex, so is by your ear piece near the top.
If you have changed housing, then your problem will be with the microphone at the bottom which is attached to the charging port flex, there could be a few things causing a muffled sound:
- dirt in the small hole at the bottom next to the headphone port.
- microphone not placed in properly when reassembling the charging port flex, either the microphone hasn't been placed in to its slot or you haven't put the plastic bracket back in.
- adhesive could be getting in the way of the microphone at the bottom if you have put the plastic bracket back in and the adhesive has moved, or adhesive on the mesh if you moved the mesh over.
- also check the microphone itself, if none of these work, try replacing the charging flex to rule out a faulty microphone (quite rare).
(A bit of info)
There are 4 microphones on the 6s and 6s plus.
The back camera microphone is used for noise cancellation mainly, and only ever records sound when recording video.
The front camera microphone is used mainly for speakerphone conversations and Siri dictation.
There are two microphones at the bottom, the bottom left one is used for picking up your voice, and the bottom right is used to help with noise cancellation along with the back camera microphone.
So to help with the muffled sound during a call, you need to make sure there is no dirt or adhesive blocking the way of the bottom left microphone, and make sure it is inserted correctly.