Yes, it pretty much would unless you already know the game. You're missing out on a lot of HP and Boff capabilities. The Heavy Cruiser (for example) has less hull than the Reconnaissance Science Vessel (the weakest Rear Admiral ship, hull-wise), and won't allow you to take advantage of your Commander-grade officer powers.
Also, you do NOT get discounts for fleet retrofits if you purchase a lower-tier version (the Commander Thunderchild does not give you a discount on the Fleet Akira, for example).
There is a small advantage in grabbing the lower-tier/rank C-Store ships, in that whatever console that comes with it can be taking off and put on the higher rank ships. The Thunderchild's Point Defense console is very handy, particularly when leveling a character, being able to put a lot hurt in several directions. The ship itself can be used for maybe one rank higher if you keep it well geared, but not beyond that.
MOST Cmdr rank ships won't survive in ESTFs. The Borg just do too much damage. One of the only ships I would dare even try it in is the Cmdr Excel, since it's pretty tanky, but tbh, I hate that ship, so I will stick to my Oddy and Chel'gret thanks much.
In normal STFs, you can win in a Type 8 Shuttle. That's how pitiful the enemies are. Also normals are facerolls requiring very little brainpower and only mk VI weapons. Basically Normal STFs are a joke, and should NEVER be used as a test on what works and what doesn't. And anyone who sticks to just normals shouldn't post on what works and what doesn't.
Is there a reason to grab Cmdr level ships from the C-store? YES. The unique consoles they come with are sometimes VERY awesome (especially on the KDF side). Other than that though, not really. You're better off getting a VA ship.
And for the record, you only get a discount on a fleet ship if you have the VA c-store ship, NOT the Cmdr level one.
It is said the best weapon is one that is never fired. I disagree. The best weapon is one you only have to fire... once.