Generally speaking they have the same problems as the mainstream distros, but with the additional caveat of even less chance of googling solutions and worse or no support at all from non-oss software.
> LVM can make two disks appear like they're one, but of course if you remove any of them they both fail. Doesn't really solve the underlying "I want to install apps outside of the root partition" problem though.
Precisely. The very concept is just so foreign to most of the Linux community that even talking about it gets you strange looks. It is actually possible to do with some significant AUFS-fu, but its a hell of a hoop to jump through for functionality that is pretty natural in every other desktop OS that ever existed.
[0] https://en.wikipedia.org/wiki/GoboLinux
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What you describe is like installing in $HOME. It's not unusual - python virtualenv, ruby rbenv, node_modules. This comes with trade off - either system knows where to search or one has to define per project. By FHS entire Linux tree is a project. In Windows... configuration is pain.
Flatpak someday.
└── gems
├── irb-1.2.3
│ ├── exe
│ │ └── irb
│ └── lib
│ ├── irb
│ └── irb.rb
└── rack-2.2.2
├── bin
│ └── rackup
└── lib
├── rack
└── rack.rb
├── bin
│ ├── irb
│ └── rackup
└── ruby
├── irb
├── irb.rb
├── rack
└── rack.rb
I still write code in a Linux environment because that's where the ecosystem is, but for my daily driver I've given up on desktop Linux. And I've found that WSL gets me a Linux based development environment side by side with Windows with less pain than dual booting. I've found that when it comes to using Linux smoothly, it's a lot easier to shoehorn myself into the happy paths than to bend my setup into my way of doing things.
LVM can make two disks appear like they're one, but of course if you remove any of them they both fail. Doesn't really solve the underlying "I want to install apps outside of the root partition" problem though.