Golem mastery seems to be a multiplicative bonus for + Golem damage.
Skeleton Mage Mastery seems to work the same as Golem Mastery.
+% Skeleton Mage Damage and +% Golem Damage thus scale multiplicatively with their respective masteries.
Where exactly does +Summon damage and + Minion damage fall into the mix? Are these values multiplied in the background by mastery or do they not scale as well as +% Skeleton Mage Damage or +% Golem Damage?
Keep in mind +% means add, and x% means multiply so in that case it’s additive. This makes it pretty easy to see where the most benefit is to be gained by using a particular skill or paragon node or affix. Any ability/node/affix/whatever that specifies a single damage type (skeleton, or golem, or crit, or vuln etc) will always have a higher range than one that touches more than one damage type (damage, summon, etc). Once you’re across those two things it’s pretty easy to hunt the things that multiply, and to really focus your damage on your playstyle. Right now I’m using shadow mages but am making every effort to get crit chance and crit damage on gear, and crit damage on tempers wherever I can, because I mages doing big numbers.
I am trying to make sense of the stats screen and its interactions with minion damage modifiers.
For example, if i have 5 in Skeleton Mage Mastery for a 100%[ x ] bonus, it will show up as 100% “damage with mages” on the stats screen if no gear has “+% skeleton mage damage” and nothing from Pargon. If i add mage glyph and get the mage nodes the pragon board yields +181.1% Skeleton Mage Damage. This results in a value of 462.1% “damage with mages” on the stat screen.
462.1/181.1 = 2.5516
If i then add a piece of gear with +127.9 Skeleton Mage Damage, the stat screen "damage with mages jumps to 717.6%. Now the total added damage is -309% from gear and paragon (+advanced tooltip shows 308.8%, we can use this number because this is prob the value without the rounding).
717.6/308.8 = 2.3238
add another piece of gear with +104% Skeleton Mage Damage and “Damage with Mages” goes to 925.8% (advanced tool tips reads +412.9% from gear and paragon)
925.8/412.9 = 2.2422
At +816.4% Skeleton Mage Damage from gear and paragon, the sheet value reads 1732.8
1732.8/816.4 = 2.1225
At +8 Skeleton Mage Mastery (160% [ x ]) the value becomes 2.7904
As more +% Skeleton Mage Damage is added from gear and paragon, the multiplier is getting closer to 100% [ x ] from the masteries but there seems to be some unexplained math as well. Does anyone actually know the equation for net damage for minions?
Modifications to “Damage with Summoning” and “Damage with Minions” has no effect on “Damage with Mages” on the stat screen so there is no convenient way to determine how these stats behave with the Masteries.
The minion masteries are global multipliers. All or nearly all multipliers with a {x} by them are global, in fact.
In some cases this isn’t intuitive due to the way the abilities are described. Case and point, one might think “you deal 50%{x} more critical strike damage” indicates only your critical strike value is boosted by the multiplier. In reality that is not how it works. A bonus worded this way is functionally saying your critical strikes gain 50% bonus damage. Meaning, whatever value was being delivered on a crit before becomes 50% larger with the multiplier in play.
In the case of the minion masteries the bonus is applied to the minion hits and all value from them. In other words, if your mages were to deal 1 million damage with all other values then a 100%{x} bonus from mage mastery would double it to 2 million. This gets to the heart of your question. The answer is yes, +summon and +minion damage would interact with mastery multipliers.
This happens because the tooltips automatically apply relevant multipliers to the damage type. They do something like the following…
additive % x (100% + multiplier %) + multiplier %
The first part, or additive % x (100% + multiplier %), is automatically applying the multiplier to the minion additive bonus. For instance, say you had a 100%{x} from mage mastery and 100% additive mage damage. Given the mastery bonus is global it’s going to boost base minion damage and all values on it. Additive mage damage is one value on top of the base.
The second part, or + multiplier % tacked on at the end, indicates the multiplier is global and applies to other values on the minion hit.
Why does it do this, you ask? Simple, so it can toss relevant multipliers and additives into one entry in the sheet (it gets even more convoluted with stuff like iron golem sac but… yeah).
Reversing this with your listed values in the order they appear…
(462.1% - 100%) / 200% = 181.05% (game clearly rounded to 181.1% when listing add value here).
(717.6% - 100%) / 200% = 308.8%
(925.8% - 100%) / 200% = 412.9%
(1732.8% - 100%) / 200% = 816.4%
816.4% x 260% + 160% = 2282.64%
True. It’s much easier to ignore what the sheet lists for the total value, use the listed additive values (hover over value, it’s listed in tooltip at bottom) and keep your multipliers seperate to napkin math it out yourself. This is why theorycrafters and some players make spreadsheets. 
To keep track of the mess and make comparisons and decisions convenient. Then you have to test in-game to make sure things work right because many things in D4 routinely don’t.