+1
I believe there are 2 issues:
1.)
Reinforcements are always queued to the "closest planet with a factory"
Having similar issues mostly with advent, as I usually build a factory on frontline planets as they double as repair stations, though I usually have another planet further away with multiple dedicated factories.
This sometimes causes all reinforcements to be queued from a planet with 1 factory which is marginally closer, even if I have a planet 2 jumps away with relativistic factory artifact (ship build speed) and 4 factories.
2.)
The ship building is not split between systems properly,
e.g. if you have 2 systems close by with 1 factory each and you queue 10 ships, it queues 10 of them in the "closest" system, instead of splitting them 5 to first and 5 to second.
Workarounds:
you can set a rally point from your factory worlds, to your fleet, bookmark/hotkey them and build ships manually, (a-la sins 1)
this does not track them as queued in fleet tracker, but adds them properly.
Suggestions
1 Have the ability/button to "opt out" a planet from fleet reinforcement (I don't want my 1 factory planets to be considered for auto building)
pros: gives back control to the player to some extent
cons: this would cost a UI button (advanced planet actions?) and would require you to click it every time you build a factory
does not resolve issue 2 (does not split workload across planets)
2 Have the ability to override "Best Factory" to a specific planet
pros: gives back control to the player to some extent
cons: again, does not solve issue 2, where you might want to split the load between 2 planets (e.g. frigate factories on one planet and cruiser factories on another one)
3 Have the ability to associate multiple planets as "Best factories" for fleet (similar to rally point) and split the load between them
pros: gives back control to the player to some extent
cons: likely more difficult to implement (how do you split 10 frigates across 2 planets with different distances and number of factories?) and quite difficult to understand from UX
4 "intelligently" calculate how to split load between factory planets taking into account
- relative distance of planets
- ship movement speed (you can queue faster frigates farther)
- ship build speed (including artifacts)
- ship build cost reduction (tec)
- "unsafe" systems in between (enemy fleets)
pros: would be awesome
cons: getting it wrong would get you back to square 1, additionally assuming this would be extremely expensive
Addendum:
sorry, kinda overdid it 
