Hello,
Sorry to dig up an old post and too some what hijack it but I did so with the intentions to help others with is issue.
I found this when doing some googling some what about the same issue but in my case the location was in the public domain / accessible ( /home/username/whmcsdata ) but I was still getting the "The following directories are owned by a different user" error.
I added two lines to my config file an fixed the issue.
$whmcspath = '/home/username/public_html/whmcs/';
$crons_dir = '/home/username/whmcs_crons/';
https://docs.whmcs.com/Further_Security_Steps#Secure_the_Writeable_Directories