Doesn't work with Xcode tools

[FraserEmbrey]

brew config output

HOMEBREW_VERSION: 3.0.2
ORIGIN: https://github.com/Homebrew/brew
HEAD: b712bcc
Last commit: 4 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 01949e8
Core tap last commit: 8 minutes ago
Core tap branch: master
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: ["--appdir=/Users/frsr/Applications/", "--fontdir=/Library/Fonts/"]
HOMEBREW_EDITOR: /usr/local/bin/vim
HOMEBREW_MAKE_JOBS: 12
Homebrew Ruby: 2.6.3 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
CPU: dodeca-core 64-bit kabylake
Clang: 12.0 build 1200
Git: 2.30.1 => /usr/local/bin/git
Curl: 7.64.1 => /usr/bin/curl
macOS: 11.3-x86_64
CLT: 12.4.0.0.1.1610135815
Xcode: 12.4

brew doctor output

Your system is ready to brew.

---

• The brew doctor above contains no "Warning" lines.

What were you trying to do (and why)?

I wanted to use Xcode command line tools since these contain more tools than the ones installed with xcode-select --install.

What happened (include all command output)?

With the right path set and the tools working generally, brew still complains about needing to install with xcode-select --install.

Type brew upgrade:

==> Upgrading 1 outdated package:
python@3.9 3.9.2 -> 3.9.2_1
==> Upgrading python@3.9 3.9.2 -> 3.9.2_1
Error: python@3.9: the bottle needs the Apple Command Line Tools to be installed.
  You can install them, if desired, with:
    xcode-select --install

You can try to install from source with:
  brew install --build-from-source python@3.9
Please note building from source is unsupported. You will encounter build
failures with some formulae. If you experience any issues please create pull
requests instead of asking for help on Homebrew's GitHub, Twitter or any other
official channels.

What did you expect to happen?

Upgrade to just work.

Step-by-step reproduction instructions (by running brew commands)

brew update
brew upgrade

[Bo98]

I wanted to use Xcode command line tools since these contain more tools than the ones installed with xcode-select --install.

The reason we need the Command Line Tools rather than just Xcode.app is for a few reasons:

• The CLT contains more SDKs than Xcode - Xcode usually only contains one SDK, and it may be newer than your OS, while the CLT always has a compatible SDK. Having a matching SDK is very important for some formulae.
• The CLT is in a fixed location /Library/Developer/CommandLineTools while Xcode is not. This matters as some formulae (including Python) bake in paths into files at compile-time - if they pointed to Xcode then it will only work for people who have Xcode installed in the same place.

If you absolutely don't want to use the CLT, you can still build Python from source and it will use the Xcode SDK.