The National Commission for Minorities Act does not say, and basically only creates the commission which then can make decisions as to who is a minority. At the moment, an incomplete set of notifications and rules are available here, starting with the current list minus Jains. Jain inclusion is announced here, simply saying that that are acting "In exercise of the powers conferred by clause (c) of Section 2 of the National Commission for Minorities Act, 1992". Minutes of meetings (some) since Sept. 2018 are here, reporting just bureaucratic stuff and no substance. The Ministry is a subsequent creation: their available acts and rules appear to be about Waqf (Muslim charitable endowments).
Separately, the National Commission Religious And Linguistic Minorities within the ministry makes available some of their reports like this most recent one. The initial report starts with discussion of what a minority is, apparently addressing an obvious lacuna. They do state that all religions other than Hindu are minorities from a national perspective, also noting the majority status of various religions w.r.t. particular states / union territories. Under TMA Pai Foundation & Ors v. State of Karnataka, the Supreme Court held that "minority" is w.r.t. State and not the whole nation, therefore in Punjab, Hindu is a minority (etc). The Constitution only identifies linguistic and religious minorities, and matters regarding scheduled castes and tribes are treated separately. Sticking with only religious and linguistic minorities, there are numerous state acts: here is the Tamil Nadu State Minorities Commission Act, which defines minority as "the persons belonging to minority communities residing in the State of Tamil Nadu whom the Government have recognized as minorities". That commission has what appears to be a meeting-minutes (in Tamil). Here is an analogous act for Maharashtra. In other words, the initial partial classification at the national level gave way to a state-by-state classification. Disposition of smaller minority religions such as Baha'i and Santali religion is thus dealt with on a state by state basis. There is a complete lack of information answering "why" questions. The best indicator of rationale is in the reports of the National Commission Religious And Linguistic Minorities.