Qwexxion #1: Do the red pulsing lights in the port of the V1 60 still work? That's one of my favorite parts! SO cool!!
Yes, the red light works but I don't use it. I've only turned it on twice: once shortly after I bought it, when I learned it was there, and more recently when I briefly considered selling the amp. Okay, call me boring.
Rooooxaaaannne (in my best Eddie Murphy singing voice)
You don't have to put on the red light!
Qwexxion #2: What settings do you use on the R60 that the R40 can't match? Sure, the 12" w/60 watts is beefier than the the 10" w/40 watts, and 2½ times heavier, but they are also different EQ circuits!
Fender Rumble 60 manual.
The short but incomplete answer to R60/R40 comparison is that the R40 takes significantly more effort than the R60 to get a sound I like, and even then, the I find the R60 more sonically pleasing when practicing in my music room with my basses.
The more informative answer is much longer, and explains how the R40 can still be great.
R40
With the R40, the sound changes significantly depending on where I am in relation to where the speaker is pointed. The "best" sound (the one I like the most) comes when I'm straight across from the front of the amp, with the speaker raised and angled so it's pointing at my head (ears), and with the amp at least a couple of feet away from any wall. I can then dial in a nice tone with a knob starting point of 11 / 1:30 / 2:30 / noon.
However, in raising the amp from the floor and reducing bass enough to eliminate boominess, the low frequencies that give a deep, warm, pleasant-for-quiet-practice part of the tone go away.
Also, if I move off-axis from the speaker (to the left or right or standing with it by my feet, with my ears above the amp), there's significant unpleasant boominess. If I try to tame that with the bass & low bass knobs, if I then walk back in front of the amp, it sounds thin. So I keep the amp away from me and pointed at me.
I've also found that I need to tweak the tone knobs depending on which bass/strings I'm using. During most practice sessions I'll take turns with different basses, which have different strings (rounds, flats, nylons). With the R40, each will need their own dial settings to sound good to me.
R60
For the past couple of years I've been practicing standing right in front of the R60, with the amp on the floor about 5" from the wall, and it sounds great, with no boominess. I can walk around the room and the sound changes slightly but not significantly. I can also move the amp away from the wall with minimal change in the sound. The tone stays nice regardless. Something about its design just makes it less sensitive in that regard.
More recently I've started playing a bit louder (not loud, just probably now at the volume most people practice with when playing alone) and I adjusted the knobs from all-noon to 11 / 1 / 1:30 / noon, which gives me a lovely sound, retaining the deep pleasant-for-practice part of the tone.
Part of the R60's tone is this nice warm deepness (without unpleasant boom). That, with the clear mids and nice highs, makes it super easy to dial in and then set-and-forget. When I changes basses, I don't need to touch the dials. I just hear the different sound from the different strings, nicely.
BUT
But all of that is
for practice, in my quiet music room, with my basses.
When using the R40 away from home, it gets put on a stand usually at least 10' away, facing me. I only bring 1 bass with me, so no re-tweaking. Because there are other instruments and it's not super quiet (like at home), the mids matter most and it cuts through nicely. The warm nice-for-practice deeps aren't as important (and can get lost completely, depending on what other people are playing). And there's plenty of volume available. So I can 100% see how the R40 can be fun and gig-able. And the R40 is super easy to transport!
Side note:
I had an Eden Nemesis 210 that was also boomy in my music room with the knobs flat. But it has a parametric EQ, and I was able to find the "boom" frequency and reduce its level to completely eliminate any boominess, while retaining all of the "good" bass (and the mids and highs, of course). So I suspect if I had an external EQ, I could do the same with the R40.