I understand what you mean.
You cannot have the following layout:
www.domainname.com/multisiteone
www.domainname.com/multisiteone/siteone
www.domainname.com/multisiteone/sitetwo
You can have the following layout:
www.domainname.com/
www.domainname.com/siteone
www.domainname.com/sitetwo
This is a WordPress limitation. Multisite installations must always be in the root of the domain, no matter if you used subdirectories or subdomains for the sites in the blog network.
You might wonder why does Akeeba Backup lets you perform a restoration on a configuration that's clearly unsupported by WordPress. There are two reason. The first one is that during the backup extraction we don't know if you have a backup of a multisite WordPress installation (or even if you have a WordPress installation in that backup archive). This is only known after having restored the database. At this point we'd need to know if you are in a subdirectory before telling you that you shouldn't continue. However, we cannot trust the information reported by the web server because in a good 5% of the cases this will be a lie without correcting the .htaccess file's RewriteBase. This will only be possible after going through the Site Setup and Data Replacement pages where we know for sure the URL structure (or at least, we know for sure what you said it is). Well, at this point it's a bit too late to take any further action since the restoration is complete.
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!