It should vary depending on the type of resource. Farms should not struct Iron, for example, but they could struct Corn. In essence I'm saying take existing tapping capabilities and just put in a chance to randomly struct. Plantations tap Spices, but you could make them struct Spices as well, and be buildable without anything to tap. You are using 10000 for the chance to struct, which is what the mine uses. However, 1000 is also good, though it eventually gets you just a whole lot of the bonus, or something in between.
I think to do this properly, though, requires that the improvement also have some effect by itself. So, you would have camps and plantations that could be built anywhere, that would have a chance of randomly structing what they normally tap. But the AI will not build these unless they have some unique niche--it doesn't plan ahead unless told to, all it does automatically is look at yield changes. Thus the camp, for example, could be a way to build a food imp in forest.
And THAT would best be done if each population consumes 3 food instead of 2, and farms increase food production by 2. Thus cities cannot grow large on undeveloped real estate, but there are 1 food imps that help (though not really ramping up growth like farms).
I think of bonuses as being not so much something that is on that tile as something that is in a whole region, but that tile is the epicenter of it. And its not so much that the tile is the only place that resource ever is found, it is just more conducive to it. You can grow spices in a garden or anywhere, but a spice resource on a tile means that area is so conducive to growing spices--in soil, climate and other factors--that spices grow there naturally and, when properly developed, in such huge quantities they are significant to international trade.
Thus structing a bonus is learning that the area can produce it profligately, even if it has never been seen before. Perhaps a region with soil conducive to spices has never had the plants introduced, but once they are they do extremely well. Or someone digging a mine for building stone in an ordinarly hill hits a previously unknown vein of gold.