I've not been able to trigger the issue. I've tried using the tip of Org's maint branch, release_9.1.7-19-gea4cb1488 (as I mentioned above, orgstruct-mode is removed in master, which will be Org 9.2).

Right, so I have a Snakefile that looks like this (note the s/eva/eval/ to fix the typo in your original snippet):

### * imports

from glob import glob

### * rules

rule blah:
    output: "foo"
    shell: "echo blah > {output}"

### * org mode sepcific
### Local Variables:
### eval: (orgstruct-mode 1)
### orgstruct-heading-prefix-regexp: "### "
### End:

With Snakemake mode and Org on the load path and no additional configuration (i.e., emacs -Q), if I visit that file and hit tab on the imports line, it folds as expected.

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