It's not a stupid question, it's a great question. I'm probably going to screw it up with a totally confusing answer, but... *shrug*
I don't use Ejuicemeup. I use JuiceCalculator, and pondered over this same dilemma.
(You didn't disclose the nicotine level of your base, or your target nic level...)
If you're shooting for pinpoint accuracy, don't use a pre-mix.
If you're using say a 50/50 12mg base and your target is also 50/50 12mg, you'll get errors (could not add enough nic/vg to reach target) when the calc factors PG based flavors into the mix. In other words, your finished product will always be off. By how much depends on the ratio of flavors. It can be off by significant amounts if you're going above 10% flavoring.
One way around this is to use a base with higher nic than your target. That will get you to your target (lower) nic, but in doing so you're now back to having to add VG and/or PG to balance it out, which basically defeats the purpose of using a pre-mixed base.
You can custom-tailor a base to a specific flavor percentage, but then you're stuck at that exact flavor ratio for everything you make. If you tailor a base for 10% PG based flavoring, you're forced to use no more/less than 10% flavoring in everything you make. Totally impractical, and the math involved makes my head spin.
My way out of it was to compromise...trading off exactness for sheer simplicity.
My intended result is around 60/40/3mg max nic, so I pre mix at 70/30 3 mg. If I add 10% PG flavoring to that, I end up with 63/37/2.70 mg. If I add 15%, I nail it almost exactly at 59.50/40.50/2.5mg. If I add 20% flavoring (a very high ratio for me), I end up with 56/44/2.40mg...now it's getting lower in VG than I like, but 20% flavoring is a lot for me. I rarely go there.
I enter the VG/PG/nic into the calc as an ingredient "3mg base", enter it and flavors in and let it throw its errors, so I know where I'm at. My calc has default VG/PG/NIC (in whatever solution) weights pre-stored. I click "use default weights" and let it do the math.
It's a compromise, but it speeds things up so much that it's worth it for me. Honestly, I notice no difference between a 10% flavoring juice at exact ratios vs. my fudged ratios. I can't tell the difference between 2 and 3 mg nic, maybe some can.
What it looks like in my calc, notice the results box at the bottom, and the errors box next to it.
You can also simply enter the VG/PG/NIC as separate components and then add up the totals of those 3 ingredients...that's how much base you'll use. You will still be "off" by the same amount, but your calc won't tell you any of that. I prefer to do it like above, for the calc to tell me how "off" I am.
You asked about concentrate weights of flavors ("specific gravities"). So I'm to assume that you're mixing by weight, as am I. Your 1.038 is a good average, but in reality they vary. Just as an example, here's a list of Capella sg's. It's an interesting list to review, if for nothing else than you can get an idea of the flavors that use higher amounts of alcohol (the lower weights).
https://www.reddit.com/r/DIY_eJuice/comments/2kqwow/list_of_capella_flavors_and_their_weight/
Is it practical to spend hours searching out exact sg's of your flavors and including them in your calculations? I say NO, In fact, I'd rather watch grass grow than do that, and you'll never be able to find them all anyway, (take it from me, I tried). Thus your average is great.
Personally, I use a 1 ml = 1 gram constant for PG based flavors. Again, it's for the sake of simplicity. I can do the math in my head with a round number, very handy when I want to eyeball a liquid into existence quickly. Also, pretty much every mixer out there uses the 1=1 ratio. If you're following a lot of other people's recipes, it's probably a good idea to stick with 1=1, though your 1.038 will also work fine.
More important than which method to use, is to just pick a method and then stick with it, so your results are always consistent.
Totally confused now, right?
It's really not that confusing once you get your mind around it. Some prefer to practice DIY as a chemist, I prefer to practice it as a cook. Maybe someday I'll graduate to chef, but meanwhile my crazy method is working.
