Yes.
You are free you use custom server JARs, including, but not limited to:
- Spigot (including unstable beta and development versions)
- Paper
- Fabric
- Forge (including 1.17 versions without a jar file)
- Pocketmine
- Poggit
- Nukkit
- Tekkit
- FeedTheBeast
- BungeeCord (as both a hub, or servers in a BungeeCord network)