Startup variables
What the template made configurable, why some values are never shown again, and what the startup command is.
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What variables are
Every template comes with its own variables. They end up as environment variables in the container and are inserted into the startup command. Typical examples are the server file and the maximum number of players for Minecraft, or the start file and the token for a bot.
You find them under Settings, Startup variables. Each row shows the variable, its value and the template's default; Set or Change enters your own value. Required fields are marked. Variable adds your own, for example for a plugin that reads its credentials from the environment. The name consists of letters, digits and _ and does not start with a digit.
Remove takes your value away again: for a template variable, the template's default applies again; your own variable is no longer set on the next start. Only the owner of the server manages variables.
Secret values
Values saved with Store as secret are stored encrypted and never shown again, not even to you. The list shows "Secret value, hidden", and you can overwrite it with Replace. Some template variables, such as a bot token, are secret from the start.
That is a deliberate restriction. A bot token that the interface shows again on request is a token anyone with access to an open tab can take away.
Changes apply on start
A changed variable reaches the container on the next start. A running process does not re-read its environment. The files stay where they are.
The startup command
The startup command belongs to the template: it is what makes a Paper server a Paper server, which is why it cannot be edited freely. What you can influence are the variables it inserts, and Java and version via Reinstall.