Keep in mind that the signal is analog, and threshold levels trigger the AD conversion.
The AGC/filtering affects the threshold.
You only have access to the D signal after this conversion, apart from the diagnostic A output of some drives.
In theory the drive density line should not affect the filtering during reading - only the coercivity during writing -, in practice most (all?) drives we've tried changes the filtering during reading in response to density line changes.
If you think about it, it makes sense, since you want a glitch filter, AGC/low pass filter as well as reasonable readability.
What is a glitch in a DD recording can be a valid flux reversal in HD recording.
If you can't see a flux reversal for say 8us in HD MFM, chances are you missed it, while in DD MFM it's just a valid 100 encoding.
The exact filtering seems to be fine tuned by every manufacturer/model according to their preferences for the density mode selected - so even a revision of a drive model may behave slightly differently.
Hence why certain drives have no problems reading e.g. Mac disks, while others would simply never be able to read certain encoding patters correctly, as the AGC would split them.
FYI as an example, there are professionally mastered C64 and Amiga games that use encodings that are randomly readable depending on the drive (actually, head) type... and I mean on the original machines
These disks very likely did pass verification during duplication so the problem never showed until the costumer returns started flooding in.
One example from C64 is the very first V-MAX! encoded disks, that exceed the limitations of the drive, and all of them have running replacement with an encoding within the limits.
Similarly, using more dense recording, such as long tracks (either as protection or just to cram more data onto the disk) has the side effect of altering the reliability of the reading if the target drive has more than usual speed wobble or the RPM is not close enough to the ideal value.
While the PLL can track such data (the Amiga PLL remarkably well), the parameters of the PLL are set with standard recording densities in mind - so once the rotational speed diverges and the densities change from the ideal it does have a cumulative adverse effect on readability.
Regardless, using long tracks was immensely popular by game publishers - since analog copiers did not have write pre-compensation that made at most a second generation copy of a disk completely illegible.