Add a comment describing why these are disallowed.

src/cargo/util/config/mod.rs

@@ -1745,6 +1745,20 @@ impl Config {
             .env_config
             .try_borrow_with(|| self.get::<EnvConfig>("env"))?;
 
+        // Reasons for disallowing these values:
+        //
+        // - CARGO_HOME: The initial call to cargo does not honor this value
+        //   from the [env] table. Recursive calls to cargo would use the new
+        //   value, possibly behaving differently from the outer cargo.
+        //
+        // - RUSTUP_HOME: Under normal usage with rustup, this will have no
+        //   effect because the rustup proxy sets RUSTUP_HOME, and that would
+        //   override the [env] table. If the outer cargo is executed directly
+        //   circumventing the rustup proxy, then this would affect calls to
+        //   rustc (assuming that is a proxy), which could potentially cause
+        //   problems with cargo and rustc being from different toolchains. We
+        //   consider this to be not a use case we would like to support,
+        //   since it will likely cause problems or lead to confusion.
         for disallowed in &["CARGO_HOME", "RUSTUP_HOME"] {
             if env_config.contains_key(*disallowed) {
                 bail!(