I got two models(box1, tube1) in the one object(box1_object)

then I using merge node to merge these two models ( for showing in same view)

then when edit the box1 (rotate, scale etc. not using extrude or bevel) the edit node show up and link to the merge node.

I found out that I need to click the box1 node and press Enter in 3D view, then edit the object without adding the edit node.

is there any way to not click the box1 node and reach the same result?

Why not put a "transform" after box1. You won't need to hit enter in the 3D view and won't overcrowd your setup with edits.