[Te Kaha]

To answer my own question, should anyone be interested in changing the 3 mentioned commands, do the following;

1.) Disable OMEGU
2.) Backup Command.cfg
3.) Open Comman.cfg and do the following edits;

a) Change

[Cmd123]
Name=Lower_whole_periscope
Ctxt=1
Key0=0x22,c,"Ctl+PgDn"
Key1=0x43,,"C"
Key2=0x53,,"S"

to

[Cmd123]
Name=Lower_whole_periscope
Ctxt=1
Key0=0x22,c,"Ctl+PgDn"

b) Change

[Cmd137]
Name=Lower_whole_obs_periscope
Ctxt=1
Key0=0x2E,c,"Ctl+Del"
Key1=0x43,,"C"
Key2=0x53,,"S"

to

[Cmd137]
Name=Lower_whole_obs_periscope
Ctxt=1
Key0=0x2E,c,"Ctl+Del"

c) Change

[Cmd164]
Name=Ahead_standard
Ctxt=1
Str=1013
Key0=0x33,C,"3"
Key1=0x50,,"P"
Key2=0x53,,"S"
Key3=0xBA,,";"

to

[Cmd164]
Name=Ahead_standard
Ctxt=1
Str=1013
Key0=0x33,C,"3"
Key1=0xBA,,";"

d) Change

[Cmd157]
Name=Lower_snorkel
Ctxt=1
MnID=0x3F0F0005
Key0=0x43,,"C"
Key1=0x53,,"S"

to

[Cmd157]
Name=Lower_snorkel
Ctxt=1
MnID=0x3F0F0005

4.) Save and enable OMEGU.


Haven't tested the last (d) edit since I never played any campaign or mission commanding a snorkel-equipped boat.