What you tried should have worked. I just setup a test with 2 VirtualHosts for port 80 in the same conf file. This conf was in sites-available and I ran a2ensite to setup the link to it in sites-enabled
The first certbot --apache -d test1.example.com created the port 443 VirtualHost in a new conf file simpletest-le-ssl.conf. In my test the Certbot message said it was created in sites-available. I checked with ls and a symlink was created in sites-enabled.
That is different than your message which said the le-ssl.conf got created in sites-enabled
The second certbot --apache -d test2.example.com added the port 443 VHost to that same simpletest-le-ssl.conf
Is there anything non-standard in how you are using sites-available and sites-enabled?
I ran this test with Certbot 5.2.2 on Ubuntu 22