Qsys port order in the symbol file (.bsf) ... random? How to fix? (v.12.1SP1)

Not quite what you're looking for, but the SOPC Builder "version 1.1" format is produced by the Perl script in sopc_builder/bin/mk_bsf.pm Yes it looks pretty simple.

An alternate way to work around this problem is to use Quartus to produce your own .bsf file from a modified copy of your Qsys top-level .v or .vhdl file.

In other words, create a copy of the top-level HDL file, modify the ordering of the ports, and then use Quartus File->Create/Update->Create Symbol for Current File... to have Quartus parse and generate a new .bsf from your modified file.

You would only have to repeat this process each time you change the ports included in the top level Qsys.