Yes it would. The reason many do it is mostly because the people or the guides recommending it do not sufficiently explain it is an issue that should only be prominent in 2011 MBPs. Sata 6G wasn't too issue free due to insufficient insulation as it seems on the 2011 and nobody gives a sure account on the 2012.
Me I would put the SSD in the optibay. If there are any issues switch and see if they disappear or remain. If the latter it is the SSD if the former it is the SATA on the optibay.