I've already done this using Softaculous, and it seems to be working, but will I run into obscure issues down the road?
Yes you can, but the "gotcha" to look for are the default htaccess rewrite rules that wordpress uses. With them the "front" wordpress is going to try to parse all url which are not mapped to actual files and therefor will mask the urls of the second site. You will have to manually edit the "front" htaccess to explicitly exclude the directory in which the other wordpress reside.
Other things to look for are robots.txt and sitemaps, especially if the front install is at the root of the domain.
Yes - no problem. You can also install multi-site and set up two different sites with one WP multisite.