Examples of Muslim nations/government/constitutions guaranteeing freedom of religion while in practice they discriminate against non-Muslims, especially Jews and Christians.
Pakistan: Pakistan's constitution guarantees religious freedom, but the country's blasphemy laws are often used to target religious minorities, including Christians and Jews. These laws carry severe penalties, including the death penalty, and are frequently misused to settle personal scores or to incite violence. Christians and Jews face discrimination in various aspects of life, including employment and access to justice.
Egypt: While Egypt's constitution protects freedom of belief, Christians (primarily Coptic Orthodox Christians) face discrimination and violence. They often encounter difficulties in building or repairing churches, and they are sometimes targeted by extremist groups. The government's response to such incidents can be inconsistent, and the legal system may not always provide adequate protection for religious minorities.
Iran: Iran's constitution recognizes religious minorities, including Christians and Jews, but they face significant restrictions. Christians, particularly those who convert from Islam, are often subject to harassment, arrest, and imprisonment. Jewish communities also face limitations and discrimination. The government tightly controls religious activities and expression, and religious minorities are often excluded from certain professions and positions.
Malaysia: Malaysia's constitution guarantees freedom of religion, but Islam is the state religion. Non-Muslims, including Christians and Jews, face discrimination in various areas, including restrictions on religious expression, proselytization, and the use of certain religious terms. Conversion from Islam is often difficult, and religious minorities may face societal pressure and discrimination.
Source: Religious Freedom Report. United States Department of State.
This is quite clear. You are "free" to have whatever religion you like. But just as "freedom of speech" does not include "immunity from the consequences of exercising your freedom of speech", the Muslim nations' so-called "freedom of religion" does not include immunity if you exercise your religion.
Words have meaning. The US Constitution First Amendment is quite explicit that it guarantees the "free exercise" of religion. These other nations do not do that, and that's the difference.