Ext. function clash when using 2 externals plugins

Hi,

Is it possible to run external functions from different plugins simultaneously ?
Let me explain. If I run the following it works fine

run("Confocal Series (2.2MB)");
run("3D Manager");
run("Duplicate...", "duplicate channels=2");
run("3D object counter...", "threshold=67 slice=12 min.=2000 max.=4000000 objects");
Ext.Manager3D_AddImage();

But the following fails (I guess) because Ext.Manager3D_AddImage() is for the 3D manager but CLIJ is run between run("3D Manager") and Ext.Manager3D_AddImage().

run("Confocal Series (2.2MB)");
run("3D Manager");
////////////random stuff
run("CLIJ Macro Extensions", "cl_device=");
Ext.CLIJ_push("confocal-series.tif");		
/////
selectWindow("confocal-series.tif");
run("Duplicate...", "duplicate channels=2");
run("3D object counter...", "threshold=67 slice=12 min.=2000 max.=4000000 objects");
Ext.Manager3D_AddImage();

So my question is, is it possible to run those different plugins without needing to initialize them just before using them ? The reason is that I need to run both CLIJ and 3D roi manager sequentially twice and a few thousand times, so it is quite time consuming to initialise them then closing them twice each per file I need to process.

Also every time I close the 3D roi manager, according to the window menu it is still thereā€¦Is it normal ?
image

Thank you very much