The problem I have is that it makes no logical sense.
1) This is purely an assumption on your part. When evidence suggests this condition actually occurs in a real fighter and is the cause of lower thrust at high altitude?
2) What relevance does high altitude and LOW speed engine performance have for supercruise optimisation? At altitude and Mach 0.9+ engines typically need smaller intakes than they do at low speed - typical fighter inlets are sized for optimal operation at precisely high subsonic speeds, which is smaller than they would ideally be at low altitude and slow speeds. That's why they sometimes have blow-in auxillary intakes, though as Whitford suggests an undersized intake can ingest larger volumes anyway if the engine is turning and sucking the air in. At very high speeds, lots of the air entering the intake is typically dumped straight out of bypass doors because it's not needed by the engine. Note that the Lightning with its seriously undersized intake was designed that way to optimise it for low drag at supersonic flight. I don't see how an argument can be constructed that a extra large intake is some kind of supercruise adaptation.
1.
Via Stack Exchange.
So you have a few things going on here.
-First, exhaust velocity is relatively fixed, although increased pressure increases the velocity further.
-Second, theoretical max thrust decreases as the aircraft goes faster.
-Third, mass flow to the engine decreases dramatically with altitude, holding speed constant.
To put into perspective how air density (and thus mass flow) changes with altitude, check out this graph:
2. I'm just using it as an example of how an engine-inlet system can choke.
mass flow rate = density * velocity * area.
Note that mass flow rate is linear with respect to velocity, and not a square.
An engine has a fixed mass flow rate requirement, but the actual mass flow rate is going to vary depending on speed and altitude.
The practical issue with inlet design for supercruise is that you have three fields of control; the speed of the aircraft, the variability of the inlet, and the fixed design of the inlet (with the variability being a component).
With air density varying by 400% (~25% atm at ~10,000 meters), designing inlets for supercruise with bad engines means that you want near-optimal mass flow rate at a given altitude and speed.
On the other hand, the mass flow rate creates a separate limitation. If your mass flow rate through the inlet is too high, you'll have to bleed off the air, creating drag instead of thrust. This could, for instance, make it impossible to take off if you're optimized for too different a flight regime than ground conditions. And even if you do take off, your lift to drag could make it impossible to ascend to sufficient altitudes, although the situation should improve as you get higher.
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Just to put things in perspective again, this is the Su-27 AL-31 dry thrust graph at various altitudes:
What kind of speed and altitude does the Su-27 AL-31+inlet combo seem optimized for? The AL-31 and its inlets seem very much optimized for low-altitude cruise when dry. The situation likely changes dramatically when afterburners are turned on, however.
More likely, an insufficient mass flow rate and low dry thrust at altitude is actually a designed-for feature, since lower thrust implies lower fuel consumption and thus more efficient cruise.