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It’s pointless to lump together all the factors that affect randomness in the game; this way you won’t get anywhere.
You need to compare the development of two Mage Guilds at opponents’, keeping everything else equal.
No one disputes that things like the availability of necessary resources, hero skills, and the overall presence of a city with a level 5 Mage Guild can influence the outcome of the game – these are also factors, but they are independent of the concept of rebuilding itself.
In other words, if skill were determined by the combined speed of building/rebuilding the Mage Guild and the effective use of acquired spells, then it would be logical to balance the probabilities of obtaining spells in the Mage Guild.
One obvious drawback is that if something like the Fresh Mod option is implemented, inappropriate trading will begin on maps such as 6LM against cities without a level 5 Mage Guild. Otherwise, it seems that, given everything else being equal, synchronous rebuilding of the Mage Guild should have an equal chance of obtaining the desired spells, i.e., equal probabilities.
However, this is not the case now, simply because of the different number of level 5 spells in cities.
Limiting the number of rebuilds to obtain the desired spell seems logical because there is no point in performing more actions than necessary.
TL DR
I support the option implemented in Fresh Mod, including taking into account the zero probability of obtaining a control spell from the first rebuild. Because every time you build a level 5 Mage Guild, you must rely not on luck getting Dimension Door on the first try (without further plans for rebuilding), but on calculating that with N rebuilds you will get Dimension Door (with a plan to collect resources for rebuilding).
P.S.
For those interested, I made a comparative table of the probabilities of obtaining Dimension Door with the Nth rebuild. The main idea is that the most likely event occurs last, i.e., the worst-case scenario was considered.