I'm really still not so sure about this. The Governance techs give bonuses to "Total Manufacturing". The icon is an orange hammer, which is the manufacturing icon. Now granted, those bonuses do not show up in any planetary tool tips so it's not immediately obvious in the UI how it is applied. So I won't say I'm certain, but based upon what I see in game, my guess is Total Manufacuring != Production.
Well, find your base outputs before modifiers. I.e. take a planet, set the manufacturing fraction to 100%, read off the raw manufacturing and remember it, then do the same for wealth and for research. If "total manufacturing" bonuses apply to production, then the raw manufacturing, gross income, and raw research numbers should be identical. If the "total manufacturing" bonuses apply only to manufacturing, then raw manufacturing ought to be higher than the other two unmodified output types. If you really need to convince yourself that the bonus isn't not shown in the tool tips but is applied with the other bonuses (either before or after), figure out the multiplier to manufacturing and then multiply the raw manufacturing by that. If the raw manufacturing output multiplied by the multipliers shown in the tool tip gives you the manufacturing output shown on the screen, then the "total manufacturing" bonus clearly isn't being applied after everything else to manufacturing, either. If you still aren't sure after that, the production model in v1.02 is
[total production] = (1 + [approval modifier] + [other production modifiers])*([flat production bonus] + [population])
The approval modifier runs from -0.25 to +0.25, though what exactly it is you'll need to determine with a curve fit using the data points given in GalCiv3GlobalDefs.XML since the production modifier from approval no longer matches the approval modifiers to any of the other planet attributes, if I'm not mistaken. Add everything up and see where you think "total manufacturing" bonuses go. Hint: they're production bonuses and modifiers.
You don't even need to go that far into the game to test this; Colony Capitals and the Civilization Capital each give +5 "total manufacturing," according to their tool tips. The planets have identical maximum raw manufacturing, raw research, and gross income values before the bonuses listed in the tool tips are applied, these values match the expected value of the planet's production under the assumption that "total manufacturing" is a bonus to production (remember to include the approval adjustment which, just like every other thing associated with production, isn't displayed anywhere), and these values multiplied by the planet's bonuses to the appropriate output type match the listed output on the planet, so clearly the "total manufacturing" bonuses from the colony and civilization capital are not being applied to manufacturing output.
If you look into the XML, you see that the colony capitals have the following effects:
<Stats>
<EffectType>ProductionPoints</EffectType>
<Target>
<TargetType>Colony</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>5</Value>
</Stats>
<Stats>
<EffectType>GoodsAndServices</EffectType>
<Target>
<TargetType>Colony</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>3</Value>
</Stats>
<Stats>
<EffectType>InfluencePerTurn</EffectType>
<Target>
<TargetType>Colony</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>1</Value>
</Stats>
<Stats>
<EffectType>Food</EffectType>
<Target>
<TargetType>Colony</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>5</Value>
</Stats>
<Stats>
<EffectType>SensorRange</EffectType>
<Target>
<TargetType>Colony</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>5</Value>
</Stats>
Goods and services is clearly Morale in game; food, sensor range, and influence are obviously not the"total manufacturing" mentioned in the in-game tool tip, which we can readily determine is a bonus to production. We do see a +5 "production points," which matches nicely with the +5 "total manufacturing" displayed on the in-game tool tip, and which we already determined to be a bonus to production rather than manufacturing.
Checking the Durantium Refinery, we see that it offers the following primary effect:
<Stats>
<EffectType>ProductionPoints</EffectType>
<Target>
<TargetType>Colony</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>2</Value>
</Stats>
On the Colony Capital, this effect was used to provide a production bonus and was listed in-game as "total manufacturing." This is the same effect type in the XML, and it has the same tool tip in the game. It seems reasonably likely that this is in fact a production bonus, not a manufacturing bonus, despite the claim made in the tool tip; checking the numbers in the game will probably confirm that, though I see no reason to bother doing so again.
Checking the Thalan Hive, the Thalan Mother Hive, the Durantium Refinery, the Colony Capital, and the Civilization Capital improvements, the Enhanced Production and Interstellar Governance techs, and the Economic Ring starbase module, we see that all of these use the ProductionPoints effect type for the bonus which gets listed in-game as a bonus to "total manufacturing." Factories, the Productive faction traits, and the Relentless trait all use the MaxManufacturing effect type, and all show up in game as bonuses to manufacturing output, with the bonuses being listed in the tool tips. It is very clear that the bonuses claimed within the game to be to "total manufacturing" are in fact bonuses to production.