First, you want to sort files numerically counting optional minus sign, which you won't do with command you show.
Second, you talk about PageLabels for PDF pages, which you can add using Ghostscript and pdfmark
operator.
Try this command:
ls src/*.png | \
sort -n | \
convert @- pdf:- | \
gs \
-sDEVICE=pdfwrite \
-o out/book.pdf \
-c '[{Catalog}<</PageLabels<</Nums[0<</P(-3)>>1<</P(-2)>>2<</P(-1)>>3<</S/D>>]>>>>/PUT pdfmark' \
-f -
It's for 3 pages -3, -2 and -1, followed by any number of pages labelled 1, 2, 3 etc. Modify according to your needs.