The B-36TC is indeed fuel injected. And turbocharged. The alternate air door should be "sucked" open anytime the air filter becomes clogged enough to create a differential pressure across the filter sufficient to overcome the spring tension holding the alternate air door closed. IIRC, the alternate air door should open with a delta P of only a couple inches Hg.
The interaction between the alternate air door actuation, turbocharger, fuel injection servo and waste gate controller has the makings of a fine esoteric technical discussion. But I'd need to get my hands on the manuals to make a case I felt comfortable with. It's quite possible that the mixture ratio could be affected in this scenario, possibly leading to engine roughness or reduction in power output. The devil is in the details.
westhawk