Will these foods for IEM disorders and hypoallergenic formula for allergenic conditions fall under the scope of Second Schedule (for standard pack sizes) under Legal Metrology rules?

No. As per order vide WM-19(60)/2016 dated 14.12.2016 of Legal Metrology Division, Ministry of Consumers Affairs, Food and Public Distribution the pack sizes prescribed in the Second Schedule of Legal Metrology (Packaged Commodities) Rules 2011 are not applicable for products covered under this directive till 14.12.2017.