It's really only price sensitive *and* low volume that cares about that. It's not surprising that they don't cater to that market.
Even that becomes less of a problem thanks to the folks like JLCPCB, which make higher-layer count PCB tech more accessible. If someone would tell me two years ago that now I can have 10 layer PCBs manufactured with via-in-pad for ~$200, I wouldn't believe it, and yet
here they are. The only thing that's holding me from going all-in to 0.5 mm BGAs is their lack of support for 0.08 mm traces, which is a requirement for fitting a trace between via field, and/or of course blind-buried vias, but I can't see how they can implement this with a shared-panel approach.
Also if you are low volume you can probably use one of their partner SOMs. At least for what they call "midrange" and above, you can get an entire SOM with voltage regulators, DRAM, flash memory, and board to board connectors in single unit quantities for less than the FPGA itself in unit quantities. Obviously in higher volumes you don't actually pay the digikey price, and for "low end" parts like the spartan US+ the cost of the SOM parts is a bigger fraction but it still can be an attractive option for low volume.
SOMs have their own problems in a sense that they limit what you can implement. If your application happens to fit with what SOM offers, that's good, but in my experience most of my designs relied heavily on the fact that I can customize memory interface parameters (bus width, capacity), in one case I actually needed two separate DDR3 interfaces (which you will never find on a SOM). And of course fully custom designs tend to be more compact (high-speed connectors are typically by far the largest parts on a board, so you have a ton of PCB space by just NOT having them), which sometimes is also important.