As someone who owns two aluminum-cased Filcos, the main downsides I see compared to a Korean/custom winkey board are lack of LED lighting, no possibility of off-center Caps Lock, and no option for Cherry stabilizers. I purchased one of the cases full retail from mechanicalkeyboards.com and added it to a Filco I already owned and purchased the second keyboard with the preowned case. I know for a fact that there is no way in hell I could own two Korean aluminum boards for the same price, and that the initial $150 purchase/upgrade to my stock Camo Filco made me decide that I would look for another secondhand Filco rather than lust after a Korean board.
If you want to use winkeyless vintage Cherry sets, have customized LED lighting, experiment with switches constantly, or build something from scratch (if you so desire), your only option is custom. Those are things a stock Filco will never do, and only one of those things can be solved by a plate swap (which adds complications by making you fabricate standoffs if you want to use them in an aluminum case). Plus, there is no denying the design of Korean boards like my personal favorite, the 356L.
BUT!
If you just want a winkey board, like Co-star stabilizers, don't want LEDs, and really just like your basic Filco but wish it didn't have a creaky plastic case: Buy a metal case. Filcos are nicely made keyboards out of the factory, I'm not sure why everyone is so keen to chop them up so quickly. You can set them up with a spring/switch combo of your liking with a soldering iron, but don't be expecting to pop tops for easy repairs if you pull a stem or your OCD kicks in and makes you want to lube your sliders again. A Filco with a new case is pretty much as close to a fuss free keyboard as you can get after popping the warranty sticker. There are no issues with firmware or programming or anything, it is as simple as it was from the factory in a shiny and heavy new dress.
Basically, know what is important to you about the keyboard. If you want winkeyless, you have no choice, you have to go custom. But if you want a winkey board, think about how much deviation from the norm you want in the finished product, and then go from there. I decided that backlighting and an offcenter Caps Lock wasn't worth the $100+ difference in cost between the full MSRP of the Filco and case compared to something like a KMAC ($410 without switches for the unassembled kit). I did want to get into the Skeldon Phantom case buy to have a metal case for my phantom kit that is collecting dust, but that was going to be $350+ for a case once anodizing, shipping, and fees were complete. I think it's cheaper than people expect to get into the realm of metal keyboards. A used Filco and used Vortex case are sitting in independent listings in the classifieds for $110 and $120 respectively, so you can technically get a working metal-cased keyboard for $230 and shipping (even cheaper if you want to put in a QFR with a replacement USB cable and deal with the empty LED holes in the case).
So yeah. Custom keyboards are cool, and offer things unavailable from larger-scale manufacturers. However, I love my two Filcos, and see no logical reason to "upgrade" either to a Korean custom. I hope options like the Vortex case are more common for QFRs and Filcos, because the increase in stability and general imposing mass of a metal case really does make them feel rock-solid.