I’ll chime in with the others voicing the opinion that she may have been amused, but her comment sounds like she was trying to be pleasant and encouraging. Her response certainly was not mean or insulting!
I presume the rest of your presentation was male? If so, the contrast was likely what both drew her eye and elicited the amused comment.
If it was me, I would approach her at the next opportunity, dressed in your normal male street clothes, and tell her, “Ummm, hey, I just wanted to say that I appreciated that you weren’t mean or insulting to me when you spotted me the other day, going for a walk in a skirt. Thank you. You’re the first neighbor who ever noticed. I hadn’t expected anyone else to be out at that time, and… it startled me. That was why I ran off. This is a relatively new experience for me, and I really don’t want the whole neighborhood talking about it, okay? But if you want to talk to me privately about it, that’s cool.”
See where it goes from there. She might well become a supportive ‘gal pal’ ally, someone who can give you an honest feminine opinion about your style choices, maybe even help you shop discretely for new stuff. And if you’re both single? Might be the start of something nice!