When I start neovide from my applications and run :checkhealth I get errors that node and other commands are not available. But when I start it from my terminal there is no error for those commands. I tried to copy and modify the neovide desktop file to start just nvim and see if there if something wrong with my my neovide installation. But also starting just nvim as application prints the same errors.
I'm using linux with plasma desktop
TL:DR; add a path variable
Depending on your configuration, nvim will need to know the environment to run some executables (like it is with node in your example). An easy solution is to add the path variable to the exec command in the according .desktop file. I remember that I had the same issue with node not being recognized in a configuration using my plasma installation. On gnome node was recognized and healthchecks were good, so I thought I didn't need the extra path. Later on I realized that I had trouble with other commands. E.g. when using fdfind to complete path commands. Again I had to search what the reason was and it also was the missing path.
To give an example, let's say you are using zsh and want to start neovide with multigrid enabled, the Exec line in your desktop file could look like:
Exec=zsh -c "source ~/.config/zsh/.zshrc && neovide --multigrid %F"