The fix for https://bugs.openjdk.org/browse/JDK-8315657 solved the issue of JavaFX applications staying in the background after they were launched.

After that fix, and on macOS 14.0+, when apps are created via jpackage, launching them from their shortcut icon works fine, as they get to the foreground and are properly activated.

However, when they are launched from the command line, they get to the foreground but they are not activated, and the user needs to click on them for that, otherwise, the activated application is still the Terminal (or IDE) app from they were launched.

For a quick test, install SceneBuilder with JavaFX 21.0.1 (from https://github.com/gluonhq/scenebuilder/releases/download/21.0.1-RC/SceneBuilder-21.0.1-RC-aarch64.dmg or https://github.com/gluonhq/scenebuilder/releases/download/21.0.1-RC/SceneBuilder-21.0.1-RC-amd64.dmg).

Launch SceneBuilder from the shortcut icon:
(from shortcut.png)

Launching SceneBuilder from command line with:
$ /Applications/SceneBuilder.app/Contents/MacOS/SceneBuilder
(from commandline.png)

This can also be reproduced easily launching any JavaFX application from command line:
java --module-path ... --add-modules javafx.controls myApp
mvn javafx:run
gradle run
...

With some debugging, it can be seen that the launching process stops at applicationDidFinishLaunching:

 [main:0] Java_com_sun_glass_ui_mac_MacApplication__1initIDs
 [main:0] Java_com_sun_glass_ui_mac_MacApplication__1runLoop
 [main:0] waiting for [glass started]
 [main:1] GlassApplication:runLoop ENTER
 [main:0] waiting for [glass started]
 [main:0] waiting for [glass started]
 [main:0] waiting for [glass started]
 [main:1] GlassApplication:applicationWillFinishLaunching
 [main:1] Java_com_sun_glass_ui_mac_MacApplication__1isTriggerReactivation
 [main:1] Java_com_sun_glass_ui_mac_MacApplication__1getScreens
 [main:1] Java_com_sun_glass_ui_mac_MacApplication__1getVideoRefreshPeriod
 [main:1] CVDisplayLinkGetActualOutputVideoRefreshPeriod: 0.016667
 [main:1] GlassApplication:application:openFiles
 [main:1] GlassApplication:applicationDidFinishLaunching

so these are missing:
[main:1] GlassApplication:applicationWillBecomeActive
[main:1] GlassApplication:applicationDidBecomeActive