I just had an idea for balancing Tinkerers, ironically based off that exploit mentioned earlier.
Remove the Tinker line of skills. In its place.
Disk Technician: You are skilled at crafting items from their blueprints. However, you can only follow the plans, not innovate on them. (No chance for special attributes, however would have a slightly lower intelligence point to acquire then tinker 1. Can only craft with disks, not actually learn them.)
Tinkerer's Memory: You can commit all but the most advanced data disks to memory. In addition, the act of crafting from memory allows you a better understanding of the gear you make, allowing for customization and increased yields. (Can learn what are now tier 1 and 2 recipes. Good chance of getting at least one bonus attribute to gear crafted, with a somewhat poor but still possible chance of getting multiple bonuses. Any recipe that does not have a chance for modifiers has a chance to increase the yield, a 50% chance for each item the recipe normally makes. So, for example, the lead slug recipe normally makes 5 slugs. Each slug made gives a 50% chance to make an extra one, for a possible yield of 5-10 slugs. Grenades and tonics have a 50% chance of getting an extra out of the deal, which helps when you're dealing with rare materials to make said tonics from. Should have a requirement around the tinker 2 level, if not slightly higher.)
Expert Tinker: You rank among the best tinker's in the Qud. You can commit all recipes to memory, and have will make exceptional gear. (Always get a modifier on crafted gear. Non modifier items always produce extra amounts. High chance of multiple mods on a single piece of gear. Intelligence point should be higher then tinker 3.)
Skill points for the first should be lowish, letting non intelligence based characters get access to it reasonably early, at the cost of otherwise useful combat skills. Skill points for the other two skills should be higher then the current tinker skills, to further emphasize the mad scientist kills everything with uber weapons motif. Oh, and you only get bonuses when crafting from memory, to avoid the ability to simply use a disk a few times for a super weapon, then sell it back to someone.