and -a is described as: -a autosplit mode with -n or -p (splits $_ into @F)

yes, but you ommitted the -a switch from your 2nd one-liner.
You didn't need it in the first one because you explicity declared @F

The following works fine for me:

ls -al | perl -F// -lane '$i=0; @a = map {$i++%2 ? $_ : " "} @F; print
+ @a;'
[download]

Cheers,
Darren :)