That code block goes into your /var/www/wiki/ folder, and should be newly created as:
.htaccess
It doesn't go into the site.conf (or default.conf file if you are using that).
In the site.conf or (default.conf file if you're using that) file, you just want to make sure that wiki.site.com is pointing to /var/www/wiki, not /var/www/html, which is often set as the default.
https://www.digitalocean.com/community/tutorials/how-to-set-up-apache-virtual-hosts-on-ubuntu-16-04 covers the other steps you want to peek at that address how you want to handle the site.conf file (and any other *.conf files) specifically.
This covers .htaccess and how to get it going, which has a bit more info than the other link. https://www.digitalocean.com/community/tutorials/how-to-use-the-htaccess-file
Between those two tutorials, I've been able to get multiple wikis and a default index page landing running off of one droplet, with each site in it's own folder in /var/www/ with things pointing where they need to be pointed to get people to the right places.
EDIT FOR EXAMPLE:
For an example following the two tuts above:
https://pantheogenesis.world/
https://www.pantheogenesis.world/
https://forum.pantheogenesis.world/
...and while these have nothing on them/done to them yet, note the footer text, which demonstrates they are each distinct wiki installs:
https://core.pantheogenesis.world/
https://7d.pantheogenesis.world/
https://7dstaff.pantheogenesis.world/
I puttered out and stopped giving a fuck before finishing up the intended interwiki links to pipe the data around, but eh. (The goal here is to store all RPG data on core to pipe to whatever game wiki is active as needed, with each game having a private staff wiki and a player-side wiki that can all talk to each other in a fairly fine-grained way.) They otherwise share some core files with symbolic links to what would otherwise be needlessly duplicated data; this is all stored in 'core' and linked to 7d and 7dstaff, to control edit permissions and access to data on the various wikis as needed. You don't need anything from this latter paragraph, probably, but the two linked tutorials explain all the steps needed to do what you're trying to accomplish above.
IMPORTANT: Note that if you choose to use no additional text or swap in place of index.php and just go straight from the domain to the content, you will need to lock down the main namespace so no one can edit it to prevent potential conflicts. This means using custom namespaces for your various categories of things rather than dumping everything into the main namespace. Doing this also gains you access to the DPL namespace=<whatever> selection criteria, which may help prevent the need for as many categories on the wiki, and allows you to use the categories for more fine-tuning in your queries.