I have the same name as a self-published author. I am afraid I will be confused for this person. Should I indicate in my query that this author and I are different people?
Yes! While I don't try to find dirt on queriers, it's entirely possible I will have heard of someone else with your name, particularly if they are well known, or active in publishing.
Thus you write "Thank you for your time and consideration, Felix Buttonweezer (not the self-published Felix)"
You see why it's ESSENTIAL you have your own website. The link you include in your query shows me you are not a published (self or otherwise) author.
I don't assume queriers are trying to mislead me by saying they aren't published if they have been. If that's the case, that reckoning is down the road, and it will be pretty terrible (in other words, don't lie about this.)
If your name is also that of someone you'd prefer NOT to be associated with (your folks, the lovely Mr and Mrs Manson, really liked the name Charles) you can always use initials, or a pen name.
In the case of my wonderful client Stephanie Evans, who writes traditional mysteries featuring a Church of Christ Minister, she was a bit taken aback to find the OTHER Stephanie Evans was a stripper. That's why my Stephanie is now Stephanie Jaye Evans.
Short answer: yes, you should distinguish yourself. There are several ways to do that, you can pick the one you prefer.