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Hello! So this one is finally one I know a bit about - electrical - so hopefully I can give you guys ample information in this first post.
I have a 2004 Honda Civic Si 2.0L Hatchback with a Charging System Error light(red battery light) thats been on ever since I bought the car. I have replaced the alternator myself with 4 different ones(under warrantee) that were all confirmed charging before and after being put in. Light remained lit throughout all of this. I then read to try unplugging the 4-pin connector from the alternator and turning the key to ON. Light remained lit. I then started the car for maybe 10 seconds. Light remained lit.
Next up, instrument cluster diagnostic mode. In this mode, the battery light did turn on and off with the rest of the lights.
Next im thinking grounding problem maybe? I cleaned the two main grounds coming off of the NEGATIVE battery terminal. Light remained lit.

So this is what I genuinely consider the fun part where I get to check for electrical wiring problems on a vehicle(ive never done this before on a car).
Just a rundown for those who dont have access to the wiring diagrams:
(Keep in mind I may be wrong with some or all of this. Im not a trained professional)
Alternator plug has 4 wires(WHT/GRN, WHT/RED, WHT/BLU, BLK/YEL).
BLK/YEL is switched with the ignition to battery positive.
WHT/GRN goes to the ECU(pin B18) for "ALTERNATOR CONTROL SIGNAL"
WHT/RED goes to the ECU(pin B13) for "ALTERNATOR FR SIGNAL"
WHT/BLU goes to the ECU(pin B10) for "ALTERNATOR L SIGNAL" and signals to the ECU to turn on the battery light by grounding this wire

Continuity/Resistance check with a multimeter shows all wires had continuity from the alternator plug to the ECU connector except for WHT/RED(ECU pin B13) which had no connection at all. I ran a new wire for that and spliced it in. The Light remained lit.
I then unplugged both ends of the wires(ECU & Alternator plug) and tested each one for continuity with ground. None did.

Any ideas before I throw $600 or whatever it is at a new ECU and programming it?

 
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All aftermarket alternators?

 
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Correct. From what I understand the one that I got with the car that was throwing the light was the original alternator that came with the car. They could have been lying to me though for all my knowledge on that goes. I've heard here and there that this light will be shown unless you use a OEM alternator. Is there any reasoning behind why that keeps getting said? It's going to be expensive and difficult to find one. At that point I'd just emulate what it wants with a micro controller on the ecu pin side of things. I just want the light to go away honestly lol.

 
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Honda's dont like aftermarket electronics. Find a used oem one or suck it up and pay for a new one.

 
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While I have heard that a bit, I've also read elsewhere on multiple Honda forum threads(maybe this forum?) That if I unplug the 4-pin connector and the light stays lit then it's not the alternator.

EDIT:
I guess it was you who said it, so maybe there was some conflicting info back then in 2017 here

 
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Many cases in here that problems are solved after installing OEM alternator...

 
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Is there a place you recommend to get a non-used OEM? I'm not even sure where to look. And I've been unable to find a EP3 in any junk yards near me.

 
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Car-part.com for junkyards. I'm sure there's other models besides the ep3 that use the same alternator

 
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Found the OE manufacturer for my car's alternator according to multiple Honda warehouses. Name is Denso. Found one on Amazon for CHEAPER than the part store one so I bought it and put it in. Lights off and we're charging! Thanks guys!

As a cherry on top, the parts store is willing to refund me for the original alternator I bought in full no fuss.

Again for SEO, 2004 Honda Civic Si with Denso alternator from Amazon makes charging light go off.

 
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Rockauto lists it as well

 
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I would just avoid parts stores as much as you can.