Hi Timmy,
Thanks for using Microsoft products and posting in the community, I'm glad to offer help.
According to your description, I did the following steps on my side:
1.
Create a classic team site
2.
Enable "SharePoint Server Publishing Infrastructure" in "Site Collection Features" settings
3.
Enable "SharePoint Server Publishing" in "Site Features" settings
4.
Enable custom script via PowerShell (the same command as yours)
5.
Create an "Enterprise Wiki" subsite under this team site
6.
Edit the page and the Content Editor and Script Editor webparts are available.
And I also tried creating an Enterprise Wiki site directly instead of subsite, it worked as well.
As we can see, you seemed to have done everything that needs to be done, but the two webparts are still disappear, to better narrow down the cause, could you please check whether they are available if you are working on
other pages instead of an Enterprise Wiki page?
Besides, you can ask your colleagues to see if they encountered the same problem, so that we can know if it affects you only or your entire tenant.
Sorry for the inconvenient to your work, I hope the above information can help you a little, please feel free to let me know if there is any progress, I'll continue to help you.
Best Regards,
Arck