First let me say welcome to the community! Glad to have you join us!
I may be wrong, but it sounds like you're using an older shared hosting plan as the issue described is something commonly encountered on Classic/Web hosting plans. Because of the configuration of these environments, they usually use separate FTP servers (nodes) for access. Depending on the nodes associated with your account, your CLI will most likely only have 5.2/5.3 available as very few of these were updated with 5.4.
If you absolutely have to have 5.4, you might consider moving your site to a Linux cPanel shared hosting plan. These new hosting plans we currently offer allow you to select
PHP versions 5.4, 5.5, and 5.6. Also, the version specified in the panel works for both web and CLI.
If you're trying to use this within different type of hosting plan, please let us know. If it's outside of the plans that I suggested, perhaps another member would have a better idea on how to work around this.
CG - GoDaddy | Community Moderator 24/7 support available at x.co/247support