Boutique to me implies "small shop" as opposed to the "big shops" like Boss, Ibanez, etc. Or if we're talking guitars, a Suhr or an Tyler would be boutique, and a Fender Custom Shop guitar not. In essence, you can apply the term "boutique" to pedals made in a "small shop," whether by an individual or a small team of builders.
"Boutique" might imply that much time and care was put into creating the product, from concept to pcb layout to component choice to box art. However, it doesn't always imply that the circuitry is original. In many cases, the circuitry is just a modified variation of another well known circuit. Take Landgraff's Dynamic Overdrive for instance, it is pretty much a modded clone of the TS808/9 in a fancy box. If you look at the guts, however, you can't help but think "DIY".
If you think about it, a number of boutique builders are making the pedals themselves, which in a way is DIY. Take Lovepedal for instance, Sean makes the Eternity pedals himself, which technically makes the pedal a DIY. The only difference is, he doesn't really make it for himself but instead, for a buyer.
Something else that "boutique" does not always imply is quality, be it build quality, circuit design, etc. I'll use Landgraff again as an example, if you've ever seen the guts of the LOD, as I have said, very DIY looking. In fact, some DIY pedals have layouts and wiring that are much better quality than the LOD. Another example is the Xotic BB Preamp. It is a great sounding box but it is missing one very simple feature: input RF filtering (then again, a great number of efx circuits are also bereft of this often overlooked feature). In spite of these seemingly insignificant shortcomings, both pedals are still categorized by some as "boutique."
One observation I've had suggests that it is the buyer (or the market) that affixes the term to a product. In my case, some of the individuals that I had built pedals for were the ones who labeled my creation as boutique. I never called my work as such.
