currently taking courses working towards my CPI, While I was visiting a friend I asked to look at there water heater and furnace, the water heater made sense, but I was left with a few questions regarding the furnace and its duct work, first off I am curious to if the AC supply air connecting to the main plenum and the side take off directly below it is of concern, further more is this maybe why there a vent fan?
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If they’re both supply ducts it’s a lousy install. Normally the branch take offs come off the top or side only.
Any chance one is a bypass for a zoned system?
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With only the info you have given, it looks like a basic supply side duct connection feeding one or more registers. The fact it is a basement register doesn’t mean much. At least in my area, basements are usually conditioned and have supply/return registers.
What exactly is your concern? Maybe I’m misunderstanding the question. 
I can’t see why it would matter. The air doesn’t know or care which direction the take-off is. You may see them on the top or side more just for head clearance purposes, but it won’t affect the airflow either way.
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Try not to overthink things. Read the illustration. “Duct to basement heat register” No more, no less.
Heat supply Register. Below is referred to as a register that is mounted to the subflooring.
Duct. Supply and return duct work come in many shapes and sizes.
Vent fan where? And why do you think it is related?
Where are you located Travis?
Was this in the basement?
I see 2 trunks, I’m guessing by the limited visibility, that one is a supply and one is a return.
It looks like possibly there was an addition in the basment and someone added a supply duct to the trunk (labeled basement heat) and hacked it.
Also the ducts that are labeled “basement heat” & “AC supply” deliver both heat and AC, depending on what the controller is set at.
As for the switch labeled “fan”, did you turn it on and off to see what it energized?
I’ve never seen a fan/blower that had a seperate switch/disconnect from the furnace.
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Guide to troubleshooting heating system furnace controls, limit controls, and fan controls.
I really see switches of this type, set up this way.
Screws are loose on the switch cover plates.
And even more alarming, the screw head slots are not aligned vertically. Amateurish. 
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Typical AC furnace setup up forced air winter / summer setting for supply and return. Heat rises, cold air settles.
Maybe it’s a bad angle in the pic, but duct take-offs should generally not be opposite each other, you lose the static pressure faster in order to deliver the right amount of air elsewhere.