It will still end up at SCOTUS.
I wouldn't bet on that. This is hardly new territory. The Supreme Court (and lower federal courts of appeal) is notorious for booting separation of powers cases for a variety of reasons. The reason people think
this conflict is a groundbreaking separation of powers conflict is because the numerous prior instances either happened long enough ago that most people don't remember or care (like any news cycle) and/or didn't get nearly the same media coverage.
How many of those overrode the will of Congress?
Was there any objection to any of those declarations from a majority of any chamber of Congress? No president has ever resorted to declaring a National Emergency to be able to fund a completely partisan policy.
Here's a perfect example of such a case:
Sanchez-Espinoza v Reagan, 248 U.S. App. D.C. 146, 210 (D.C. Cir. 1985), which was brought by members of Congress against the Reagan Administration, arguing executive overreach in violation of the Appropriations Clause based on Reagan's use of treasury funds to support the Contras in Nicuragua in violation of the Boland Amendment (specifically forbidding use of fiscal appropriations to support the Contras), and further contending that Reagan's use of the funds violated the War Powers Clause, which delegates Congress with the power to declare war. The case was dismissed on the grounds that it presents a "nonjusticiable political question."
That last phrase may ring a bell to some of you that were paying attention in high school history class. The "political question doctrine" was laid out by the Supreme Court back in 1803, in the famous case
Marbury v. Madison, 5 U.S. 137, 170 (1803), wherein the Supreme Court wrote: “[q]uestions, in their nature political, or which are, by the Constitution and laws, submitted to the executive can never be made in this court.” The Supreme Court has since established various factors for determining whether a dispute implicates political question doctrine (generally outlined in
Baker v. Carr, 369 U.S. 186, 217 (1962), I won't restate them here unless someone wants to read them), the presence of any of which will cause the court to declare the controversy a nonjusticiable political question.
To that end, federal courts
routinely decide that separation of powers controversies invoke the
political question doctrine, and thereby constitute nonjusticiable political questions. They also repeatedly emphasize that the judicial branch is not suited to analyze and enforce issues of budgeting and accounting. I cited one example above involving a challenge to actions taken by a Republican President (Reagan) "against the will of Congress," and here's one involving a similar challenge to action taken by a Democrat President (Clinton) "against the will of Congress."
See Campbell v. Clinton, 203 F.3d 19 (D.C. Cir. 2000) (upholding dismissal of suit brought by members of Congress challenging President Clinton's act of war in Yugoslavia after Congress voted down declaration of war, emphasizing that Congress has the means necessary to remedy their grievances, i.e., by passing new legislation prohibiting use of appropriated funds for specified purposes, etc). The Supreme Court declined to consider it on further appeal (certiorari).
Campbell v. Clinton, 531 U.S. 815 (2000). See also
Chenoweth v. Clinton, 181 F.3d 112, 115 (D.C.Cir.1999) (emphasizing the separation-of-powers problems inherent in legislative standing, and holding congressmen had no standing to challenge the President's introduction of a program through executive order rather than statute).