This is what I understand from the information I have read on the matter. I haven't read the actual laws. That would be boring.
A brewer's license gives permission to brew beer and sell that beer on premises. This is what we know as the "tap room". They can only sell the beer that they produce. No beers can be purchased and sold by the brewery.
This license has several restrictions insisted on by the MTA when this law was passed. Only 64oz of beer can sold per person per day. This is the dreaded 4 pint limit. They must stop serving beer at 8pm and be closed for business by 9pm. Also, there is a production limit. If the brewery produces over a certain amount, they can no longer charge for the beer they sell in-house. An example of this is Big Sky Brewing, the maker of Moose Drool. If you have ever visited their brewery in Missoula, they give away free samples. Kettle House brewery also in Missoula has reached this limit and has decided to cap production in order to keep their tap house open for loyal customers. No more Cold Smoke Porter at Toppers in Helena.
The retail license which gives permission to buy and sell alcohol. Grocery stores and gas stations have a retail license.
The MTA wants breweries to purchase a retail license, increase the restrictions to the amount of beer that can be sold in the tap rooms. Also, prevent them from selling any food or other beverages, or having any type of entertainment. You wouldn't even be able to order in a pizza. No pool tables, darts, no soda, candy bars, or free popcorn in the tap rooms. These tap rooms are the bread and butter of the micro-breweries and the additional restrictions would essentially put them out of business or severely limit profits.
Then we have the Beer/Wine license, and Liquor license which are issued on a quota system based on population. The MTA lobbied for this system a while back to basically inflate the price of a liquor license. These licenses are transferable when a bar or restaurant is sold, adding possibly millions to value of the establishment. This system also limits the profits of other restaurants by preventing them from selling beer and wine, and prevents new bars and taverns from opening if there is no population increases in a community. When was the last time a new bar opened in Miles City? The MTA also tried to get rid of the BYOB law so people can't bring your own bottle of wine to places that don't have a license to serve alcohol.
Sorry for the long post.