I’m guessing that companies like Eventide, when they want to become price-competitive in the marketplace against small innovator-companies, radically drop their component-part quality in order to keep making bank.
In this case you apparently got a pedal where they’d done this. As it’s a ‘face’ vs ‘function’ issue, they’d gamble on you not complaining because it basically works.
It can be like this, yeah.
If the rust will stay on a level where it’s now — I can live with it 100%. But now I mostly concerned about what is going on inside the device 
I’d do treatment to seal it where it is, once oxidation starts it’s not going to stop by itself.
Inside I would not be concerned. I haven’t taken apart an H90, but I have opened up some other pedals to flip internal switches and I work on most of my old game consoles. Inside, you’re not going to have many steel parts that will rust like this, with the possible exception of a few standoffs. Even those I’d expect to be brass, which won’t rust. Copper, gold, and aluminum are the metals you’d mostly see inside, and they don’t rust when they oxidize. I don’t know what Tin sauter does off the top of my head, but that will only be used to mount a few through-hole parts (likely the I/O ports, the footswitches, and the rotary encoders). That’s more likely to crack from old age and need to be reflowed than it is to rust.
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+1 for WD40 - apply sparingly with a cotton bud stick and wipe off the surface excess. It should settle into the porous parts where the rust has been arising. Try to avoid getting it on the plastic parts, obviously.