Are boutique amps just another amp in the end?
There are plenty of reasons to go boutique. The most important is to get an amp that's not otherwise available in current production. For example, if you really want an old blackface or tweed amp but don't want to deal with the costs of ownership of a 40 or 50 year old relic...
There are also boutique amps that offer unique designs. Some that come to mind are Dr. Z and /13 amps. These guys aren't copying anyone, so you get a chance to try something totally new.
Finally, boutique amps are built to higher quality standards than most production amps.
As to whether they're "just another amp in the end", I'd have to say yes. Not because boutique amps don't have some intrinsic value; they do. As I said above, a boutique amp can give you a reproduction of a classic design, a modern designer's take on the future of guitar amps, or a higher-quality product. But in the end an amp - any amp - is just a tool to help you make music. If a boutique amp works better for you, then that's what you should use. But there's nothing "wrong", per se, with a standard production amp. Look at what the pros use: you'll find top-notch players in both camps.
Finally, I have to point out that there are diminishing returns to putting money into more expensive amps. At the core, all guitar amps are pretty much the same. The designer's choices are constrained by the technology and by players' expectations. As a player you may prefer a more expensive amp for many reasons, but whether a listener can discern the difference between a $300 amp and a $3,000 amp is highly debatable.
I've spent several full days in the company of good players who own a wide range of amps, many of them boutique. It has been quite an education. I don't hear dramatic differences between amps of similar architecture (for example, amps based upon classic designs vs. modern high-gain designs). It's true that some of them are voiced differently than others. But in the end I hear the player, not the amp.