Rasputins Rage said:

No, gems and runes have no effect... Remove prior....

'have no effect' is not quite correct.

In transforming equipment from one to the other, any current gems are destroyed (so, as he notes, have no effect). It specifically warns you against that, and gives you the opportunity to cancel the process so you can.

- if you have enough of them, just go ahead. [This is rather common.]

- if you know you're just crafting it on the way to something else, just don't add the gems in the first place.

- it can be useful to hang jewels off this intermediary equipment in the mean time, while you work on other (intermediary) equipment.

= -8% (epic) > -0% while working on -8% elsewhere. -8% x 12 >> -0%

= on the last one, remove the -8%, add it to the 3 other epic's you have waiting to make legendary, then reapply.

=- i.e. On the last 4 pieces you still have epic, the next legendary you acquire, gives you epic 1 of 4 for the last piece. Rinse, repeat.

There is some advantage to having legendary armor of each type, any armor - to give you something to hang jewels off of.
[If not legendary, don't bother. Boosts too little to be material, and you're just going to re-do it to get legendary, anyways. Especially as you need legendary armor to hang legendary jewels on.]

e.g. Hang study and training jewels off Adrian equipment while working on raising your Sixtus.

(12 x -10% = non-trivial)

Or silver boosts off your battle gear while you're working on your build gear. And/or vice versa.