Audi Concert to Alpine 8RX from PDF.png
This is the basic sound system config with the Concert and Symphony head units (the Chorus is similar, but has only a 2x 20w amp and is only paired with the 8RE sound system without the rear speakers). This is what the Alpine directly slots into, with the Alpine 4-ch internal amp driving the same speaker configuration as the Concert 4-ch internal amp.
Audi Concert to Alpine 9VD from PDF.png
This is the standard sound system config with the radio head units (not supported with Chorus). In this config, the radio units are coded to low output power, probably just skips the voltage gain stage. But regardless of how it was implemented, you still get four "speaker" outputs. I assume the fade and balance is still processed by the Concert, and would be seen in the different voltage levels of the four outputs. The processing of the center and sub signals from these, and the removal of the sub bass from the four main inputs, would be done at the J525.
For the Alpine, it could have directly slotted in for the Concert, but it appears the Alpine has no switch to drop the output voltage for the amplified outputs. Which isn't surprising, that would be a very abnormal scenario for an aftermarket radio unit. If one wanted to use low level signals, one would just use RCAs. But this is integration into a factory configuration. Though I have to wonder, what if one ran the RCA outputs to the J525 input pins. It's all just "voltage". Still, for whatever reason, the Alpine solution is to run a resistor block on the speaker outputs before it joins the factory harness on way to the J525 inputs.
Beyond that, I can't really say since I'm not sure exactly what it is you're trying to remove and trying to add. The tweeters in the factory config have a cap for some basic bass blocking, but that's it. If you're replacing the factory 2-way speaker pair with an aftermarket set, I assume you'd source or implement some quality 2-way crossover config matching the two drivers well. But none of that requires doing anything with the electronics. The Alpine amp channels are 50w peak into 4Ω 9(iirc); the standard sound system is 40w rms to the fronts, which I believe is a 2Ω woofer and 8Ω tweeter. I'd probably stick to the J525 amp channel, until you're ready to add aftermarket amps.
At which point, the Alpine probably runs the RCAs and speaker outputs at the same time. So run the RCAs to a 2-ch amp to drive the front pairs and leave the speaker config as is to run the rears, sub, and center. Then just disconnect the front speaker wires from the J525.
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