First of all, deleting those troops from the mapfile is fairly easy, since it is all in one place inside the map file. For convenience, I attached an edited mapfile with starting locations being outside cities, i.e. each player starting without these troops.
That said, in the original mapfile these troops serve as defense for the cities, who should be focal points of the map. There is no other option to strengthen the defenders of a certain province.

The population type does only influence the availability of recruitable troops, not the type and numbers of the actual defenders. Therefore I placed them by hand, which then leads to nations start with these troops.
However, I think this is fair as everyone starts with the same troops. Thus one gets a quicker start on
even terms, which is something I do like (for having more than one starting province is not advisable on my map, as many cities are adjacent!). Furthermore those troops are easily available to anyone holding a fortified city anyway.
The mages were just added for fun. But now I think that they might balance things as well: I do not like it that finding a single magical site such as a library is such a huge advantage. So everyone gets two those independent wizards for free, boosting research a bit for everyone. (One might consider difficult research as well) Furthermore, their random paths cannot be taken into account at pretender creation, so a player has to adapt to what he gets and has to deal with these options (I really liked the randomly assigend predesigned-pretenders in the Shepherd's Scenario).
Also, I do like the idea that these three commanders are rather unique and thus present a nice prestige goal for assassins...

Same holds for the Cavalary, or how do you obtain those again bearing your home province's name? I have fun by using them cautiosly and nuturing them to high XP as my pretender's elite bodyguard...
In the end, it's everybody's own choice whether to play with the troops or not: I like them, as long as nobody convinces me that they shift the balance in favor of the powerhouses Caelum, Vanheim, etc,..