Taking a step back to the OP...
Mesa is not quite priced in the boutique market but close enough. You get a lot of amp for a reasonable price. Sure, over the years the prices will increase. All companies do this as the market changes, cost of materials go up, wages go up, etc. Considering what I paid for the JP2C in 2016, it was expensive but much more affordable than they are now. Ouch. So, consider that the PCB assembly is mostly hand inserted components. Relays, capacitors, transistors and the like. The resistors could be machine inserted or done by hand as well. That would be the wave solder assembly line. Number of workers to build the PCB for soldering the components. I doubt the preamp tube sockets are run through the wave solder line, that may be soldered by hand as they do sick out on the bottom side some distance from the board surface. Hand soldering of all of the lead wires, then comes the assembly of the PCB assembly, chassis and control features, jacks, etc. I could only imagine the time it takes to start from raw parts to build one complete assembly. It is quite an involved process and that requires labor hours to do it. I am surprised that the Mark V90 does not cost more than the Mark VII or JP2C considering the overall size of the preamp and power amp boards and other board assemblies for the GEQ and back panel. The Mark V90 has more of the boards exposed so you can see most of it. The power tube board is on a different level than the main preamp board. The Rectifier tube board is also separate. Also, due to the nature of the beast, it would not be possible to do this on a peg board with like they used to make them in the 1960-1980. More features and circuits, the more complex the assembly to achieve it. The chassis is a formed aluminum sheet and then welded to ensure a good rigid structure. It also goes through a painting process. I would not doubt that the chassis is a purchased component from a good resource. That bezel on the front panel is also a machined aluminum plate that gets anodized black after it is processed. The Mark V90 is truly a work of art and sounds good too. The sum of the parts and labor of assembly will drive the cost up.
The cost of the head is now $3145 as listed on Mesa's web site. I am sort of tempted to buy one as the one I have now has had some issues. Plus, I am so familiar with it, I know what preamp tubes makes it sound really good. I would be curious to see if they made any changes since 2012 (I hope so).
Just for S&G, lets take a look at an amp that retails now for $2600. The EVH 5150 IIIs EL34. This is made in Mexico by Fender. It only has six preamp tubes. External power capacitors so it appears they can be replaced when needed. I would say this is comparable to the Mark V90 in some ways. The front grill is made of 3 layers of cut sheet metal. It becomes rather delicate once you remove the screws, it has to be removed to get the chassis out. (same with the rear panel).
Here is the innards image, There is so much wasted space on the PCB. the components few compared to the Mark V90. So I would ask, why is the EVH product so expensive based on what little you get shoved inside it. Just about every component is attached to the PCB, not much in hand soldering except for the factory mod of bypassing a gain stage to use CH3 circuits with CH2.
If I had to rate the quality of each, the Mark V90 wins hands down. Not because it is a Mesa product, more so, how it is made and how it sounds.
Now we can see the smaller boxed amps like the JP2C and the Mark VII. There is a gut shot of the JP2C It makes use of all of the triodes of each preamp tube. What you can't see is buried under the main preamp board. Well, this was made specifically to be as close to the original IIC+ HRG in its characteristics. It is not an exact replica as most of the components used back then are obsolete. A few added features like the midi controller and cab clone. Not as many relays as that used on the Mark V90. Getting the JP2C all sfuffed into the smaller enclosure looks to be more time consuming. Taking the assembly apart looks to be more of a nightmare than the Mark V90.
And now for the Mark VII, Mesa wanted a similar role of the next mark amp to have as many features or voices as possible, somewhat like the Mark V90 that has 9 unique voices. The Mark VII only has 7 voices (two are repeated). Let's use the same chassis as the JP2C and stuff more into it. This took some planning and the JP2C was the starting point. Again, we are seeing several layers of stacked boards so not all is in view like it is with the Mark V90.
For a brand comparison but different model, Here is the MWDR. Not as expensive as any of the large bottle Mark amps. Still it is busy with many components. Currently sells for $2700. Much simpler in design, not as packed as the Mark V90 or the other amps.
You get what you pay for when it comes to Mesa. Sure, I wish the prices were a bit more affordable. I have no regrets paying what I did for each amp. I feel that the EVH was over priced for what you get. I can see why the Mesa products are more expensive but what is inside is what counts the most. Not only are the guts made of quality parts, the other materials on the outside are of better quality then I have seen with other brands. I want something that will last the test of time. The longest period I owned a single Mesa product was 24 years and sold it to a friend about 13 years ago, it is still going strong as it did for me over the 24 years of ownership. Not sure how the EVH will fair on the long haul, I barely ever use it.