Unfortunately it's a limitation of the Android platform; you can't add arbitrary launch activities at runtime. So the Chrome team is unable to fix this AFAIK.
However, you could imagine a future release of Android that sports a custom homescreen app that just includes Chrome progressive webapps in the main app drawer. Or someone might be able to write a third-party homescreen app already that does that. (Not sure if Chrome exports that data though TBH.)
Also, FWIW, the "add to homescreen" is really just icing on the cake - even without it, PWAs save data locally and are launchable offline. If you remove Pokedex.org from your homescreen, you'll notice you can still navigate to https://pokedex.org while in airplane mode, and Chrome still reports some 6MB of Pokémon data as being stored on your device. (It remains to be seen whether this is a bug or a feature... but we'll see how many PWAs abuse it.)
The Chrome team should tell the Google Now Home activity team to show these apps in the drawer until they get the Android team to implement runtime (instead of install time) addition of launcher activities. It sounds like an instance of UX failure through non-communication.
Unfortunately it's a limitation of the Android platform; you can't add arbitrary launch activities at runtime. So the Chrome team is unable to fix this AFAIK.
However, you could imagine a future release of Android that sports a custom homescreen app that just includes Chrome progressive webapps in the main app drawer. Or someone might be able to write a third-party homescreen app already that does that. (Not sure if Chrome exports that data though TBH.)
Also, FWIW, the "add to homescreen" is really just icing on the cake - even without it, PWAs save data locally and are launchable offline. If you remove Pokedex.org from your homescreen, you'll notice you can still navigate to https://pokedex.org while in airplane mode, and Chrome still reports some 6MB of Pokémon data as being stored on your device. (It remains to be seen whether this is a bug or a feature... but we'll see how many PWAs abuse it.)