Another consideration, is that refineries are built with a certain grade of crude oil in mind.
For example several refineries along the Gulf Coast were built to process the very heavy sour (high sulfur) crude from Venezuela. They produce a lot of asphalt and roofing tiles, but they are not well suited for processing very light and sweet crude oils, like Saudi, or what we get from fracking in America.
Yields, and thereby profit margins, will vary, processing different crudes at different refineries. Many can’t or won’t process certain grades.
Russia’s main export oil is their Urals grade. It is a mix of heavy sour oil of the Urals and the Volga region with light oil of Western Siberia. That mixing requires and extensive (and vulnerable) infrastructure, across vast distances (many time zones). The great distances are a major factor in why the Power of Siberia 2 natural gas pipeline has not been funded - more than a thousand miles of it would have to transit wilderness, where there are not even any roads.
Not all the refinery capacity, or the crude oil can be interchanged, making for more concentrated/specialized points of vulnerability than otherwise.
Refineries are not built often. After the fall of the Soviet Union more than 30 years ago, most Russian refinery construction was conducted by the International Oil Majors, with a lot of the expertise and manufacturing capacity for many key components residing outside of Russia.
Since the collapse of the Soviet system, there has been a dramatic reduction in the scale of Russian technical education. The depth of their bench for engineering expertise is nothing like it was during the late Soviet Union. That trend has accelerated sharply during the current invasion, as education and health care have been the biggest bill payers in the Russian budget trying to cover the wartime deficits.
Restoring damaged refineries is likely going to be a non-trivial challenge for Russia, and there is no way that they could possibly keep up with the huge scale and rapid pace of refinery damage, if current trends continue. Just since this thread was started a few days ago, three more refineries have been successfully struck and set on fire - Novokuibyshevsk, Syzran and Perviy Zavod (a Military facility).
“Since the collapse of the Soviet system, there has been a dramatic reduction in the scale of Russian technical education.”
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It seems like the Kremlin is sufficiently satisfied in just teaching the children of Russia three things: revisionism, delusion and the love for never ending wars.
The education needed to make the Russian nation go forward towards progress and new inventions seems dead now.