Not really... Most people use the pc case on the right side of the monitor. So if you lock the case to that position, you just need to face the acrylic panel and IO to the opposite side (left). Also, you have the option to put IO on top, which I personally prefer, and you said it's a cheaper solution.If i will go with side i/o locking the case in one position will be not a good idea because if you will put your case on your desk in that position that the i/o will face to an wall you can't use it.
Anyway, just a last feedback I would like to give: I know the unibody approach is a backup for now, but I really think you should consider it as the definitive one in the future. The external of the unibody design reminds the A4 a lot, which is very good the way I see, cause it creates a brand identity. Also, it looks much cooler to me, but I know not everyone will agree.
Cheers, and good luck