Is it acceptable to apply to a masters program based on your weakness, rather than you strength?
Your reasoning is excellent and I would suggest you stick with this approach: All educational programs exist to increase the knowledge and skills of the student, which presupposes weakness relative to the outcome of the program.  Remember that you need to convince the admissions committee that your undergraduate record is strong enough to justify admission to the Masters program, but at the same time, it is your intention to focus on up-skilling in your areas of weakness, with a view to becoming sufficiently competent for entry to a PhD program at a later time.  There is no contradiction in these two things - your existing set of skills from your undergraduate program might legitimately be considered to be strong enough for entry to the Masters program, but weak in comparison to how you will come out (this being the entire  point of education).

In terms of assessing postgraduate applicants, this is generally the kind of student I would prefer --- one who is able to look at his/her existing skills in a realistic way, identify weaknesses, set goals for improvement, and be proactive in plugging those weaknesses to achieve goals.  Would that there were more students like this!