It does have lower output, so you would need more gain to maintain the same volume level, but 3.5V is still high output, so I'm surprised if it is a ton. Unless you were already close to the limit of your amp at 4.0V. Depends on your amp I guess.
I'm not an expert, but also am using a VM95ML and I have not come across these issues. For me only very few records afford turning the volume higher and only very few records seem to show more pops and clicks. So I don't think that's normal.
Yeah it sounds like it’s exposing the weaknesses in the amp and/or phono stage The better sound is it showing itself a better cartridge. Hum at a higher gain is something that exists at lower price points unfortunately.
Ah both of those have internal phono stages so you’ll be using one or the other. Are you using the one on the LP120 or on the onkyo. If you’re not using the one on the onkyo I’d have much more confidence in it that the one built into the LP120.