@thomas-weiss For anyone reading. Seems like the duet3 mini 5+ not defaulting to stealthchop anymore was the problem.
Adding a D3 to each M569 setting up the motors resolved the hissing sound.
If I missed anything that I should be doing, please let me know. 
@jay_s_uk I see - you are right. Echo to file was added in 3.4, an update should solve this. Thank you!
Sadly, we'll need our prototype for a presentation in the upcoming days and I don't want to risk that a firmware update changes or breaks any functionality that we already implemented.
Might have to go without this function for now.
Since I can't edit my last post anymore...
For the M915 I tried H-paramter from 1 - 400 and S parameters from -50 to 50.
With the following setup I got the only warning overall but I wasn't able to reproduce it at all anymore.
Warning: Driver(s) 3 stalled at Z height 0.00
Herer is my current config.g
; Configuration file for Duet 3 Mini 5+ (firmware version 3.3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v3.3.5 on Wed Nov 03 2021 10:22:11 GMT+0100 (Mitteleuropäische Normalzeit)
; Enable eventlogging
M929 P"eventlog.txt" S1
; General preferences
G90 ; send absolute coordinates...
M83 ; ...but relative extruder moves
M550 P"pt1" ; set printer name
; Network
M552 P0.0.0.0 S1 ; enable network and acquire dynamic address via DHCP
M586 P0 S1 ; enable HTTP
M586 P1 S1 ; enable FTP
M586 P2 S0 ; disable Telnet
M575 P1 B57600 S0 ; disable checksum requirement on the panel due UART
; Drives
M569 P0.1 S1 D3 V100 ; physical drive 0.1 goes forwards
M569 P0.0 S0 D3 V100 ; physical drive 0.2 goes forwards
M569 P0.3 S0 D3 V100 ; physical drive 0.3 goes backwards
M569 P0.2 S1 D3 V100 ; physical drive 0.4 goes backwards
M584 X0.3 Y0.0:0.2 Z0.1 ; set drive mapping
M350 X16 Y16 Z16 I1 ; configure microstepping with interpolation
M92 X666.67 Y666.67 Z1000.00 ; set steps per mm
M566 X1000.00 Y1000.00 Z800.00 ; set maximum instantaneous speed changes (mm/min)
M203 X4000.00 Y4000.00 Z4000.00 ; set maximum speeds (mm/min)
M201 X400.00 Y400.00 Z400.00 ; set accelerations (mm/s^2)
M906 X1500 Y1500 Z1100 ; set motor currents (mA) and motor idle factor in per cent
; Stall detection
M915 X S1 R1 F1 H10;
; Axis Limits
M208 X0 Y0 Z0 S1 ; set axis minima
M208 X150 Y100 Z55 S0 ; set axis maxima
; Endstops
M574 X1 P"^io4.in" ; configure switch-type (e.g. microswitch) endstop for low end on X via pin !^io0.in
M574 Y1 P"^io2.in+^io3.in" ; configure switch-type (e.g. microswitch) endstop for low end on Y via pin !^io1.in
M574 Z1 P"^io1.in" ; configure switch-type (e.g. microswitch) endstop for low end on Z via pin !^io2.in
; Z-Probe
M558 P0 H5 F120 T6000 ; disable Z probe but set dive height, probe speed and travel speed
M557 X15:215 Y15:180 S20 ; define mesh grid
; Heaters
M140 H-1 ; disable heated bed (overrides default heater mapping)
M950 C"out0" P0 ; setup laser to virtual outputpin 0
; Tools
M563 P0 S"spindle" ; define tool 0
M453 ; switch to cnc mode
T0 ; select first tool
And here is my homeall.g
; homez.g
; called to home the Z axis
;
G54
T-1 ; deselect tool
G91;
M17;
G4 P100;
G1 H2 X10 F4000;
G4 P100;
; HOME Z
G91 ; relative positioning
G1 H1 Z-90 F2000 ; move Z down until the endstop is triggered
G1 H2 Z3 F2000 ; move Z up a little
G1 H1 Z-5 F200 ; move Z down until the endstop is triggered
G92 Z0 ; set Z position to axis minimum (you may want to adjust this)
G90
G0 Z55 ; raise Z axis
G91
; HOME X
G1 H1 X-305 F2000 ; move quickly to X axis endstop and stop there (first pass)
G1 H2 X5 F3000 ; go back a few mm
G1 H1 X-305 F500 ; move slowly to X axis endstop once more (second pass)
; HOME Y
G1 H1 Y-185 F2000 ; move quickly to Y axis endstop and stop there (first pass)
G1 H2 Y5 F3000 ; go back a few mm
G1 H1 Y-185 F500 ; move slowly to Y axis endstop once more (second pass)
G90 ; absolute positioning
G1 X80 Y50 Z30 F3000 ; Go to machine center
The gcode I am running from SD for testing looks like this:
G90
G64
M3 S12000
G01 X20 Y50 Z0 F4000
G01 X100 Y50 Z0 F4000
; Many more of these moves ...
G01 X20 Y50 Z0 F4000
G01 X100 Y50 Z0 F4000
M5
M0
While the machine is moving, I am blocking the X axis with my hands, which makes an interesting sound when losing steps. After this, it just keeps going shifted by a few millimeter, no logs, no pausing, no execution of rehome.g (tried multiple R-parameters).
What am I missing?