That's a massive waste of resources and time.

If you are unwilling to use tools like Flatpak, then that limits what distros you can make. e.g., in a world without Flatpak, only distros with X users can exist. In a world with Flatpak, distros with X/10 users can exist.

Another way to think about it: if you want to make/use your own distro, then using Flatpak will cut down the amount of work you have to do by some large multiple. You're free to not use it, just like you're free to install custom electrical sockets in your house and make custom adaptors for every single appliance you buy.

Standardization/centralization exists for a reason.