No washers.
Here's the money question - why are you measuring the bolt?
If it's because you have mixed up bolts, count and make sure the number of matching bolts equals the available slots. Post a pic of the bolt(s) in question.
Measure again, 1 to 2 threads of engagement is a tiny amount. I've installed hundreds of that exact bolt on countless subarus with no length or install issues.
This is highly unlikely and would require significant material to bottom the bolt, but If the heads intake mating surface, or intakes head mating surface, have been filed or resurfaced or cut that would shorten the bolt path.