Since you can't create panels in standalone, you can't edit them, so I
don't think there's any way to do this directly.
However... there may be a couple way to effectively get what you need:

1) Save out a 'template' scene which has your panels configured how
you want them, but has essentially nothing else - then, instead of
creating a new file, open the template and go from there.

2) Create a script node within your scene that, on file load, checks
if it's in GUI mode, and if so, configures your panels, then deletes
or disables itself somehow.  (I seem to remember making a script node
delete itself is a little tricky, as I believe doing it directly
within the script node causes maya to crash - you have to set up an
evalDeferred or a scriptJob of some sort which does the actual
deleting...).

- Paul

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