Check manual
— ch 22 Analog inputs and
— 32.1, technical specs, analog inputs
The ports have different sensitivities / ref levels.

Ch 22.1:[…]With +4 dBu selected, the according headroom meets the latest EBU recommendations for
Broadcast usage. At -10 dBV a headroom of 12 dB is common practice, each mixing desk
operating at -10 dBV can send and receive much higher levels. Lo Gain is best suited for
professional users who prefer to work balanced and at highest levels. Lo Gain provides 15 dB
headroom at +4 dBu nominal level.[…]

Ch 22.2[…]The two combo jacks also allow for the usage of mono and stereo TRS jacks. The TRS jacks
have a fixed level attenuation of 11 dB. Based on the adjustable amplification from +0 dB up to
+65 dB, the sensitivity is +21 dBu down to –44 dBu, referenced to full scale of the AD-converter.
Therefore, the TRS inputs are true full level Line inputs, and the unit can also be used as Line
amplifier.[…]

So if you use “Low Gain” as ref level for your input channels 3-6,
then you have 15 dB headroom at +4 dBu nominal level.

My understanding is that you would need to set the amplification for Line Input 1+2 to “2” to achieve the same sensitivity of +19 dBu, comparable to “Low Gain” setting of channels 3-6.

What you also could so … Download a sinus generator and watch the Peak/RME input level in TotalMix FX, then turn the gain/amplification for Analog 1+2 so that you reach the same value as ch 3-6.