One feels like an expert by achieving expertise
Assuming that you are able to rationally diagnose your level of knowledge of the topics relevant to your work, the feeling of expertise will come with the actuality of achieving expertise. Ultimately, you will need to make a decision as to how much knowledge of this tool is useful to you, and what would constitute excessive time-allocation to learning that tool. more comprehensively. If you decide that your work does not require you to obtain deeper knowledge in the use of that tool (e.g., learning some of the things you mention) then you should accept that decision and move on to better uses of your time. However, by the same token, this would also involve accepting your limited knowledge of the tool in question. There would be no need to "overcome the feeling" that you are not an expert with the tool, because, well, you are not an expert with the tool.
In terms of the more general question of becoming confident about one's research/technical abilities, this is something that comes gradually as you learn more, produce published research in a field, teach that topic in courses, speak about it at conferences, etc. It is common to feel that you lack expertise when you are still a PhD candidate, or new graduate, and even for the first few years of a postdoc or academic position afterwards. In both cases, that feeling is generally accurate, because most people at that stage are not experts in their field. The feeling you have is merely a demonstration that your subconscious emotional responses are accurately attuned to your present level of knowledge. It is not something that should bother you at all, let alone bother you greatly.
In terms of advice, I urge you to bear in mind that a newly minted PhD graduate is not someone we would consider an academic expert in any field. Such a person is at the baseline level of competence where they are only just about to start doing research without supervision. Put your present level of knowledge in its proper perspective and proceed confident in the fact that you will learn more as your professional life evolves. So long as you work hard and make sound decisions on how to allocate your time to learning skills in your field, expertise in an area of interest will come in due time.