To answer your question, no the stitches won’t look wrong. If you look at the inside out section of my fuzzy/brushed tutorial you can see that you’re inserting the hook from inside to outside (with the hook at the back of the opening) when the piece is flipped one way, and from outside to inside (with the hook at the front of the opening) when you flip it the other way.

The right side of the fabric is still facing you whichever way you flip it, but when it’s inside out, the ‘right side’ is the inside of the back layer of the fabric. When you flip it, the ‘right side’ is the outside of the front layer of the fabric. (I know that sounds confusing, but read it while looking at the pictures and it should be clearer.)

So you’re still crocheting the same way, and your stitches will still look the same, no matter if you flip your work right way out after about 3 rounds (as I do) or just before you stuff it.

[...] Row 2: 1 Single crochet (sc)  in second chain from hook, 1 sc in each stitch across, 2sc in last stitch. DO NOT turn your work. (You want to stay looking at the front of your work – need help knowing which is the front – click here.) [...]

Ultimately, you hope that any designer would include all relevant information (like crocheting in a non-standard manner) in the pattern, but there’s no guarantee of that – some patterns only include very minimal information. If you’re unsure, try looking at the pictures of the finished sample and see if you can tell whether the stitches show the V or pi shapes (pictured above) – that’s a surefire way to tell whether it’s worked ‘inside out’ or not.

My Fuzzy to Brushed Crochet tutorial explains (with pictures):
a) why my fuzzy patterns are worked in BLO
b) why those front loops are hidden: because the fuzziest side of the work is the ‘wrong side’ according to this tutorial, so pieces worked in fuzzy yarn (or regular yarn using my ‘fuzzy’ patterns) should actually be worked ‘wrong side’ out!

And yes, the invisible decrease is only for when you’re working into both loops of the regular stitches; it doesn’t give the same benefit if you’re working into back (or front) loops only. In fact, as you’re working my fuzzy patterns ‘inside out’ anyway, the invisible decrease would leave an ugly line of unworked loops (normally hidden on the inside) on the outside of the work, so it’s definitely not a good choice!

[...] and a Clover 2.5 needle. I am really happy with how it turned out. I finally figured out this whole business with the “right” and “wrong” side, so I flipped my work and now my invisible decreases work. I only still have a problem decreasing [...]