I hate to offer another version so soon, but v.11 does fix one problem and offers a solution to another.
First, it fixes the way the trade route malus is calculated. Previously, all trade routes would count against empire health, which was never intended nor described as such in game. Now only international trade routes garner a health malus.
Second, v.11 changes the way resources impact a city's health. Previous versions added health from resources only once, even if there were multiple copies of a health resource near a city. So, for example, if a city had four nearby cattle resources, it only got +1 health. In addition, whichever city first claimed ownership of a health resource received the health bonus, even if the resource were technically closer to another city (something like the problem with the Mint). At any rate, none of this was clear in the tooltips.
With v.11, each copy of a local health resource can contribute to a city's health. Essentially, resource health yields are now like any other map yields: if a city works a health resource, it gets the health bonus. Now, as cities grow they can potentially work more health resources to offset the growth penalty. Cities can also swap out the use of health resources in overlapping tiles, allowing for better fine-tuning of city growth. Of course, each worked malus resource, like coal, iron, and oil, is additive, so productive cities will probably pay a much higher health cost.
v.11 is backwards compatible with v.10 saved games.