While you are correct in regards to general giving to the synod (50% or some percentage goes to churchwide,) I don't believe that it is true for designated giving, e.g., if the congregation designated $4000 for seminary support and gave it through the synod. All $4000 goes to the seminary and it is not figured into the percentage that goes to churchwide.
Yes, Brian, you are quite correct that designated giving, even when channeled through the synod, does not count in the mission support calculation (because MS calculus is based upon unrestricted giving). The ecclesiastical ethos in our synod, however, tends to use the mission support conduit for nearly all things related to the programmatic, operational, and granting activities of the synod--a typical pattern for interior mid-Atlantic Lutheranism.
The issue emerged for us in 2009 specifically in the area of seminary funding. Not many know the details for seminary finding, but I am happy to share.

The seminaries receive grants from the ELCA Churchwide according to a formula employing the number of ELCA M.Div. graduates and M.A.R./M.A.M.S. grads (weighted less than M.Div. grads) over a multiple year rolling average.
Synodical support uses a different calculus. Each synod is supposed to support its constituent seminary based upon aggregate congregational expense in that synod vs. aggregate congregational expense for the whole church. That calculation is done at the Churchwide office which then sends a notice to each synod for what is called "basic synodical seminary support." This amount is supposed to be remitted directly to the seminary by the synod. For my synod and most (if not all the regional synods), this amount has been a budget line funded by mission support dollars from the congregations.
In 2009, my synod was informed that our new basic synodical seminary support for the next fiscal year would be an increase of roughly $2000. Following our standard pattern--and, here, we may have been less than savvy--we were challenged to either increase our request of the congregations or cut some other budget line or some combination of the two.
Understand, if we increased our request or the congregations (without any cuts), the increase would have had to be roughly $4000 because of the proportional share requirement, meaning the Churchwide expression would receive $2000 more from my synod than would have been the case in a flat budget. Well and good if that $2000 was going become increased aggregate funding for seminaries. Ironically, the proposed budget for CA2009 included a cut in seminary funding. A little strange, don't you think, that Churchwide asked us to increase our synodical support for the seminary, stood to benefit from an additional $2000 raised in the name of theological education, which in turn would not go to theological education (compounded by the churchwide cuts at the same time).
Proportional share is just plane funky. Weird things happen in the calculus. Synods like mine are trapped in this weirdness, and, being loyal (perhaps excessively so) to the patterns and models proffered by the CNLC and enshrined in the CBCR of the ELCA, cannot get out them without violating their ecclesiastical ethos. I know that not all synods do it like my synod does (and her regional neighbors do). This is where the inequities arise. This is also why I don't think that our experience can be easily replicated. At the root of it is an ecclesiastical ethos which is not necessarily transferable. So, I maintain, the reasonable way forward is not to attempt replication but rather to admit that the ELCA is an ecclesiastical mongrel with such divergent ethoi that a per capita model offers the best approach for equity and synodical mission-mindedness. Leave off the adjustment for median family income; it unnecessarily complicates things--that way we also avoid all claims of income redistribution. Just have each synod remit an amount based upon some head count--I don't care if it is average weekly worship attendance, confirmed membership, baptized membership, voting membership, etc.. as long as it is the same standard.