Peptides which are inside of a "Protein" are always ordered by their position within the parent protein sequence. There is no way to change that order.
The thing at the top level in the Targets tree is also allowed to be a "Peptide List" which is just a list of peptides where Skyline has no idea what protein sequence they might be part of.

Peptides which are part of Peptide Lists can be dragged around in the Targets tree to either reorder them, or to make them part of a different peptide list.
Peptides which are in Proteins cannot be dragged around in the Targets tree.

In Skyline-daily, if you wanted to convert your Proteins into a Peptide List, you could use the menu item "Refine > Associate Proteins" and then supply an empty FASTA file. If you try to do the same thing in regular Skyline 23.1, then all of the unmatched peptides would end up being deleted, but in Skyline-daily the unmatched peptides will become part of one big Peptide List called "Unmatched Peptides".

I imagine you have a large document and it might be a lot of work to rearrange all of your peptides like this, but this was the only idea I could come up with.
It is possible that someone else on this support board will have a better idea.
-- Nick