Yeshiva autonomy is protected by the Constitution (under the Right to Privacy, giving parents the right to educate their children). If an originalist Supreme Court throws out the Right to Privacy, Congress would probably enact it as a statute, or propose a constitutional amendment.
Government funding from goyim is always dubious and any yeshiva that depends on goyim to stay solvent is taking a big risk. If the government were to tie funding for yeshivos to hiring unionized teachers for secular studies, most of the modern Orthodox would be very pleased.
Given the results of the Congressional elections, Biden is unlikely to do anything especially radical about any policy.