You can still do it like this. However, note that <script> tags have no order in the html and never have had - they are loaded in whatever order the browser likes. This has been true since script tags existed, so you need to be careful that your 'Game.js' etc isn't loaded before Phaser, or it'll all go wrong (the same is true for v2 though)
If you look at one of the example games, like Avoid the Germs: https://github.com/photonstorm/phaser3-examples/tree/master/public/src/games/avoid the germs you'll see it's done exactly the way you describe, where 'main.js' is the entry point (the part that the browser loads). There's no webpack or anything else here, it's just native ES6. The important part is that when you include main.js in the html, you tell the browser its a module, not a script.