A good way to test this composition rule is to run the equality analysis first, since Article 14 sets up the comparator, and then move to the autonomy analysis under Articles 25 and 26.
Start with equality. Article 14 does not forbid all classification, but it forbids classification that lacks a rational connection to a legitimate purpose. Here, the comparator group is other religious self-governing bodies, Hindu religious and charitable endowment boards, and Sikh gurdwara management committees. These bodies are generally structured to be run predominantly by, or under the effective control of, members of the community whose religious property is being managed. If the Waqf Amendment permits a Board overseeing Muslim religious endowments to include non-Muslim members beyond a proportion that would be unthinkable for those other bodies, the State is treating one religious community's self-governance right as less deserving of protection than another's, without any secular justification for the difference. That is exactly the kind of unequal, unreasoned classification Article 14 exists to catch.
Now bring in Articles 25 and 26. Article 26(b) protects a denomination's right to manage its own religious affairs, and Article 26(d) protects its right to administer property dedicated to religious or charitable purposes. A Waqf Board is the very institution through which the Muslim community exercises these two rights in practice, since it takes real decisions over mosques, madrasas, and graveyards. Diluting Muslim control over that Board by mandating a higher non-Muslim presence than the limit set is not a neutral administrative tweak, it is a direct intrusion into how the community governs its own religious institutions, which Article 25's guarantee of free religious practice reinforces since these institutions exist to serve ongoing religious observance.
Reading the equality point and the autonomy point together, the composition rule is challengeable: it treats Muslim religious administration less favourably than comparable religious bodies of other faiths without rational basis, which offends Article 14, and it independently undermines denominational self-management and property administration protected under Articles 25 and 26.