using Maschine as an FX unit in a DAW

If you're using the MaschineFX plugin as an insert: It might make more sense to do the automation in your DAW by simply by mapping some sort of control to enable/bypass maschine. This is probably the easiest.

If you're familiar with reaktor: It's pretty trivial to create an ensemble to have the audio signal switch from one output to another via midi. I made one a while ago that used the modwheel to fade between two outputs. One output went to another pad that had effects. One went out without effects. IMO, this is the most capable (but I may or may not be a reaktor fanboi).

The sequencer in maschine can't automate bypass, but you might be able to automate wet/dry. Alternatively, you could have a somewhat complex setup using sends. Audio comes into a pad 1. Put your FX on pad 2. Use a send to route audio from pad 1 to pad 2 pre fader. Now you can automate the volumes of pad 1 and 2 as your wet/dry options. You wouldn't be able to handle this via pads - it would be handled via the knobs (though I suppose you could make lock states to control it via notes coming from your DAW).

if you are utilising the maschine controller in midi mode... the desired affect can be utilised with a gated button... note events usually do this by default.... as when you hold down a note the effect is applied... it turns off when released...

to achieve this functionality inside of your host daw... with maschine as a plugin... you should be in midi mode... with your button assigned to a note.... or a gated button CC value instead of trigger of toggle... the gated value then needs to be assigned to the plugin you wish to activate... by using either the "Learn" or "auto"... this is an aspect I've found useful especially in reaper!

Maschine lock states is also a useful means of automating FX either over a period of time... ie. 1 bar 2 bars etc

lock states albeit FX states can also instantly activated at the press of a midi button

investigate Maschine lock states and you'll see how powerful it is

Thanks @LostInFoundation for mentioning my tool. I think it actually does exactly what @bosone was asking for in the original post. It has some advantages and disadvantages compared to using lock states, depending on what you are after.

So yeah, hope it's useful :)

edit: as an add-on idea, i could see a different solution as well with changing lock states by sending program change messages from another device or host app. I made a tool before in Max4Live that converts note messages to Program change messages. That could be useful for controlling lock states live too. Just see the Pattern Changer tool on this page, if you are using Ableton: