No — it's the intended trade-off, though it's easy to expect the opposite. The "Upfront fee" field on the Create Payment Link panel only appears for forms that have a hidden wpdd_token field wired up, and that hidden field is only added to a form at build time if the form was created without a fixed upfront fee. In other words, the per-link fee override and a form-level fixed fee are mutually exclusive by construction: build the form with no fee baked in if you want the flexibility to set different fees per link later; build it with a fixed fee if you want that fee to be non-negotiable and don't need the override.