Check also reference OECD11 in that second opinion report:

http://www.oecd.org/science/biosafety-biotrack/49343153.pdf

It feels like that the second opinion report is based on checking the items reased in OECD11. Take item 55 as an example related to that allergy recommendation, there is simply not enough information in literature to say that canola does not cause allergy reactions:

55. There are several published studies reporting sensitivity and allergenicity of adults to Brassica species, however, most describe rare cases of respiratory symptoms due to occupational exposure (Suh, 1998; Alvarez, 2001), or residence in proximity to areas of intense canola cultivation (Trinidade, 2010). (...) 

Again, in other words, this second opinion does not say it is unsafe, it just says there is not enough info to say it is safe.

The same reference OECD11 also refers to a Canadian company:

26. Food use of protein fractions from low erucic acid rapeseed meal has not been reported to any great extent (Tan et al., 2011). However, patents have recently been granted in Canada (e.g. Canadian patent CA 2553640) (Canadian Patent Database, 2011)), and a firm has notified the U.S. Food and Drug Administration (FDA) of certain uses of particular canola protein isolates that the firm has concluded are generally recognized as safe (GRN No. 327) (GRAS Notice Inventory, FDA, 2010).