I've watched the cost and it doesn't seem to matter at all there. Using a Magus shard to power up an Gunner character doesn't cost any more gold.
If there's a difference with the amount of experienced gained, it must be minor.
Does it really matter?
If I power up Grim Reaper Eddie - with all Magus talismans at 5 stars, only leveled up using blue runes - and only used magus shards to level up the Eddie, would the final characterbe any different than if I used random shards and runes?