Omission of "by" before gerund in imperative sentences

I have been thinking about the use of "by" and its omission in certain situations, especially before gerund in imperative sentences. I did find the other entry (“by” before the gerund, when is needed) relating to the subject, but it did not match my question.

Examples to clarify what I refer to:

• "Create a new image file by using Paint."
• "Create a new image file using Paint."

The first one feels to me as the only good option, because at least in my mind the second option makes it more difficult to understand it as fast. When I read it, it takes a while for me to understand if the meaning is "create a new image file BY using Paint" or "create a new image file WHICH uses Paint" (doesn’t make much sense though in this context, but it’s where my mind automatically goes). However, in my current job, I continuously encounter these kinds of sentences which almost always omit the "by", so I wonder if both of these forms are grammatically correct? Also, if they are both grammatically correct, is one of them instinctively easier to understand or is it just me who has problems with the second one?

(Edit.) Is there some kind of rule or other kind of mental tool I could use, so that it would be easier to estimate when "by" can/should be omitted?