I can see that, if you get decreasing returns to synergy you should have decreasing costs as well for 'off-topic' builds. The only thing is that you could maintain your bonus indefinately by pairing buildings that are synergistic with constructions that are 'off-topic'. A flat rate for 'off-topic' buildings ensures that generalists don't have bonuses.
I suppose if the bonus reduces every 'n' tiles or every 8 buildings you could allow a free 'off-topic' build. So with 500 wizards towers you could have 63 free off topic builds. Or in game terms every other time your city grew to have open slots you could build a non-synergistic building without penalty.
Also, the ideas don't disappear if left unread, but there's always more interest just after a new build. Still, synergy... benefit or burden? overpowered? The Advent in Sins have alot of synergy without any obvious cost. They can have 2 beam platforms a hanger and a repair platform. The beams increase the power of other beams, hanger provides shields and the repair platform also increases survivability. That level of synergy is overpowered. The question is how should they stack and what should the cost be? If synergy in buildings causes increased production should it be enough that you'd have to build cities that relied on each other heavily for other products or should you have a penalty for generic builds?
Should the default production of each building be lower to offset the potential maximum being much higher? say produce 6 units of food not 10 (40% reduction), but be able to get a maximum 160% bonus to that, for a max production of 15.6 (I'm thinking that the penalty should only be 1/4 of the maximum benefit. But that's just for aesthetics. It could still be overpowered, depending on how much of a no-brainer the strategy would be. Perhaps enabling positive synergy would enable negative synergy? whatever the negatives of a building are (-n% influence in galciv's slave pits, maint. costs, increased negative event chance) would increase equally but without the initial decrease.
So, a hive/telepathic collective could work with synergy on all tasks. Each extra worker in the field would give it's experience to other workers in the field and boost harvests. Every mind busy working on poetry would distract them. But equally every worker suffering in the slave pits, sacrificing themselves in the temple or generally suffering would pass on their suffering. So yes if you have a city at peace you'll have massive production. But should you need to gear up for war and build slave pits or sacrifice your population expect to have massive penalties. (maybe offset in your captital or near your sov./queen of the hive)
There are obviously non-telepathic reasons to introduce synergy. Tools, spare parts and experienced labour will be cheaper and more available in a city geared up for that form of trade than in a generalist town. Still it would be interesting to consider the following: 'is synergy overpowered? is synergy sensible?' and 'what do you gain from it?'
I'd like to think that done well it can be overpowered if you want it to be a perk, balanced for a neutral pick if you give it sufficient costs. It makes sense to be used under normal conditions and can also be used more specifically with 'hive' style races. What I think you would gain is more specific towns, each with it's own focus. Rather than a "new town" default build order like MoM (requiring an early granary for pop, maybe sawmill for increased production and a market for tax) you'd at least have a "farming town, mining town, shard town..." up to the number of unique synergy types. It'd be a good reason not to have a market/granary/sawmill in every town despite those buildings existing.