It may help to keep in mind that en doesn’t have the same grammatical function in those sentences: in one it is a preposition, in the other it is a pronoun:
En vous souhaitant bonne reception: wishing you prompt/safe delivery: here en is the preposition always going with the gérondif (En passant, en chantant, en vous souhaitant joyeux Noël).
Vous en souhaitant bonne reception: wishing you prompt/safe delivery OF IT/OF THEM. Here en is a pronoun. And the “souhaitant” is a participe présent.
Putting the full sentence of salutation, following a comma instead of a full stop, would make BOTH choices grammatically ok, because normally, you need a conjugated verb somewhere to make a sentence feel complete.
But as the other answers say, very often, that conjugated bit is part of the formalities, and nowadays just implied: those various “je vous PRIE (here is the conjugated bit) d’agréer” variations are just dropped.
Formal final sentences in French official correspondance used to be deliciously weird. It has simplified greatly, but you still see, at the end of letters, things like “Veuillez agréer, cher Monsieur, l’expression de mes sincères pensées” and other strangely obsolete looking phrases in that vein...
I personally never got the hang of all the protocol that governs it. I need to look it up check every time I write an official letter. Very codified! Your example shows the clever use of a gerund /participle followed by a full stop to just dodge the bullet!