yeah the Nano and XO cases are just re issues of the older effects placed into smaller boxes, you may not find every effect in the new smaller boxes, but the ones you do are the same as the older ones, so no, you wont lose any control options or tone there.

(with exception to the Nano Clone, but do to our complaints here in the forum it has now been replaced with Neo Clone, and the Nano Dr.Q with the bass switch is a bit off, but that just needs a trim pot adjustment and its fine!)

of the “newer boxed EH pedals i own:
Nano Clone
The Screaming Bird
The Mole
LPB-1
Dr.Q
Bass Balls
(Nano Stone on the way)

also in the larger (XO) newer boxes i have:
Stereo Memory Man W/ Hazarai
The Worm
Little Big Muff PI
Metal Muff W/ Top Boost

and many many more of the old style pedals!

so from my experience IMO, no theirs nothing wrong with using the nano pedals, or tone or control loss!

(the list in my signature was and old signal chain that really really needs to be updated, not an inventory)

it all depends on how “flexible” you need it to be.

i own the largest full model of the metal muff, but i have test driven the mid sized and nano (pocket) ones.

the smaller you go in the series, you do get less options, they all have the same distortion circuit, sound, and tone. but you lose the option to tweak the tone with an EQ, the smaller ones just dont feature, treble, mid, bass, or top boost options and controls.

** i hate to say this but….i was going to downsize my metal muff with a smaller model, but i ended up with an MXR Fullbore Metal. its the size of a nano pedal, but has all options of the large metal muff and a noise gate built in. it also (IMO) sounds way better, like a Mesa Rectifier amp in full overdrive.