Do crafting calculators include all the costs for Research Notes?

I wouldn’t assume the displayed total includes every step. Check which recipe and inputs the calculator is counting, then add any gold spent on missing ingredients or crafting fees. If a step uses a currency instead of tradable materials, account for that separately too. Comparing the full cost is more useful than relying on one total.

I’d be cautious about making ascended gear just to salvage for notes. Compare the full crafting cost with the notes you expect from the item, and check the current salvage result before committing materials. You can use the same comparison for other eligible crafted items, then try a small batch before making a large amount.