Here’s what’s happening. The head unit acts like a switch in that it switches to various audio sources. These sources include:
- radio
- Bluetooth audio
- CD
- Spotify
- auxiliary inputs from a phone
Each audio source has its own preamplifier that boosts the low voltage audio signal to the proper level for input into the amp. It really doesn’t matter is the amp is in the trunk or in the head unit; all audio systems operate this way. The differences in loudness are caused by each input’s source. That is, all amplifiers amplify at one specific level. So the CD preamp is designed to amp the CD reader’s signals at a set rate. The same goes for all of the other inputs: each input’s preamp amp’s the audio signal by a set amount. We different volume levels by changing the voltage of the main amp’s input signal.
Now, the cause of your problem is that the inputs’ to the main amp that require “turning up the volume” are lower than the radio’s inputs to the main amp.