Master effects can be controlled by the Common/Audio level assignable knobs. You can assign master effect parameters to the assignable knobs and turn the assignable knobs directly or indirectly using superknob.

I haven't explored the pattern sequencer to see which "deeper editing" is enabled or not. Namely what one can do in the Common/Audio menus in terms of parameter changing. But, in general, the pattern sequencer is designed to limit what you can edit to "control surface" type controls.

Source: https://yamahasynth.com/learn/montage/mastering-montage-modx-pattern-sequencer-features-in-os-v3

Again: Deeper editing, that is, changing/reconstructing what is available, will not be possible while the transport is running. The 28 parameters shown on the “Motion Control” > “Quick Edit” screen are available during Pattern playback. Deeper editing to the EQ, Arps or Motion Sequences will need to occur after stopping playback.

The above is ambiguous in answering your specific question, but it does show there are items on and off the "you can do that" list.

This part of the same article does cover effects in a general manner:

Warning message: “Please stop sequencer”: When using the Play/Rec function, you have restricted access to certain areas of the architecture. You will receive a “Please stop sequencer” warning message when you attempt to select functions outside of the access area. This simply means the area or function you are attempting to access cannot be used while the Sequencer transport is running. We will take a close look at what you can access in real time (during playback and recording functions).

Extra Credit: In general, any function where you are rerouting signal flow, or making a fundamental change to the structure of the Performance itself, will be restricted (off limits). If you wish to add Parts, or reconstruct your Performance data (change controller assignments, effect routing, etc., etc.), you can, but you must temporarily stop the Sequencer, return to the [PERFORMANCE (HOME)] screen, then make your additions and changes.

So if you run into what seems like a brick wall - see if you can use superknob and/or assignable knobs to change those master effect parameters.

Welcome to YamahaSynth!

how to i.e edit the master effects while running the pattern sequencer?

The short answer is: you don’t.

What you can do:
Connect the MODX to your computer via USB
Open MODX CONNECT utility
Click on IMPORT
You can literally drag ‘n’ drop each Scene into your computer via the USB connection
Using your copy of Cubase (or any DAW) you can playback the sequence data from the computer to the MODX Performance... now you can fully edit your Performance.

The MONTAGE and MODX feature a “Performance Recorder” — based on the Multi Part recording paradigm that it features.
Deep editing of the Tone Generator and the MIDI Sequence data is handle by enlisting your DAW.

MODX CONNECT allows you to drag ‘n’ drop your Pattern sequence, Scene by Scene into Cubase.
While playing back from the computer you can fully edit the Performance.

Mastering MONTAGE: Using MONTAGE CONNECT to Import Patterns

Although written for the MONTAGE, simply substitute “MODX CONNECT” for MONTAGE CONNECT.

Link to the Official MODX Downloads Page

Thanx for fast replies 😀

I think Jasons workaround "assign master effect parameters to the assignable knobs and turn the assignable knobs directly" fits my workflow best. I'm trying to use my MODX as far away from a DAW (Logic 😉 ) as possible!