[complie] Importing node modules does not work with byonm flag when entrypoint in a sub dir

[yasaichi]

Version: Deno 1.45.0 to 1.45.2

From v1.45.0, compiling files not in a root directory results in a runtime error: Relative import path "module_name" not prefixed with / or ./ or ../. Here is the minimum setup and commands to reproduce this bug.
I assume the point is that compiling files in a root directory works fine even in the latest version.

Setup

// <project-root>/src/main.ts
import { Option } from 'effect';
Option.isNone;

// <project-root>/deno.jsonc
{
  "unstable": ["byonm"]
}

Commands

$ pwd
<project-root>
$ pnpm install
$ deno compile --output main ./src/main.ts
$ ./main
error: Relative import path "effect" not prefixed with / or ./ or ../

For further details, please see this repo: https://github.com/yasaichi/reproduce-deno-compile-bug-24654