Bulk modifications: use the batch editor
Design choices: There's pros and cons for the way things are done. Preserving stored values over derived values is preferred; in this case, preserving the current EXP is preferable.
Redesign: PKHeX is open source using WinForms. Feel free to fork and re-skin yourself.
Minor details: Boring research topics for near-useless features are not in my interests. For niche tools, community research is a requirement.
Remember to consider time spent vs gain!