After quite a bit of research, I've decided to answer this myself. I believe that this was indeed meant to be a nod to the Edward Scissorhands movie and I will tell you why.
To begin I had to look into the title of the episode, The Post-Modern Prometheus. Why postmodern? What does post modern even mean? It is a relatively complex idea and there are a lot of definitions out there depending on the context but I think the best definition I could give it here to back up what I'm about to say is that post modernism is a form of using classical styles to present a style beyond modernism. Take the form of the episode. It is filmed in black and white with cliched lightning strikes similar to the style of an old Frankenstein movie. This is the key of what makes the episode "post modern" is that it brings in other styles and references to make an ironic self reference to the style of story being told. The age old tale of man creating what is perceived to be a monster when the monster only wishes to fit in.
Some examples of post modern references in the episode:
- The title of the episode is a play on Mary Shelley's "Frankenstien" subtitled The Modern Prometheus
- The black and white style is a reference to the old Boris Karloff Frankenstein movie from 1931. This was also done by Mel Brooks in creating Young Frankenstein
- The mutato's favorite movie is "Mask" from 1985 about a severely deformed kid becoming friends with the high school crowd. It also stars Cher whose music is used prominently in the episode's soundtrack.
- The original score by Mark Snow is strongly influenced by John Morris's theme from The Elephant Man, another movie about a deformed man rejected by society, and also filmed in black and white even though it was made in 1980
As you can see the episode draws heavily on the styles of other similar movies in a post modern fashion which brings me to Edward Scissorhands. I can't help but think it is more than a coincidence that both have the fumigation tent which looks very much like a circus tent and calls up thoughts of the freak show in Elephant Man. It is my opinion that Chris Carter likely had all these films in mind when making the episode and drew items like this from all of them into making The Post-Modern Prometheus.