I think the best solution I found has been to put the Southern Command HQ in Magwe, so that I always have supplies there to be used for works and for the huge quantity of AA (and CAP).
Rangoon is the entrance point and it's fine on its own.
Other bases are just moderately defended against paradrops and all the troops are in non-base hexes. Most of the troops are somewhat short of supplies but nobody has ever had more problems than in, for example, China.
The fact is that, as far as I have understood, the monsoon applies to bases. Not hexes. It indirectly leads to a relatively inefficient supplies distribution in non-base hexes as well, but if you have the "stuff which consume stuff" in non-base hexes, you are quite fine.
Also, non-base hexes should, in line of principle, be prioritized in receiving supplies: it means that they are somewhat easier to supply and that, on the other hand, supply problems in your bases are increased.