Which tarp combo would you prefer?

I would personally go for option 1.

Reason being is that the bivy covers the ground sheet and bug net option. Having the option to place a quilt or bag into the bivy in rain spray or buggy nites is nice to have (On warm non buggy nites i just place my bag ontop of the bivy)

Also using the shelter without a bivy, tested that theory 'again' last week in Desolation wilderness. I can confidently say after, weathering pretty fierce afternoon t-storms sporadically throughout the week, in a 5×8 integral designs sil tarp, using an equinox bivy as a ground sheet(not placing the down bag inside at all), I stayed dry, my bag stayed dry, and my sanity stayed dry!

Well I'd also go option 1, as overall I would agree it is probably more weather worthy. Its also better to use for muddy conditions from what I hear. If you want a bigger tarp for the same weight, you could find a lighter bivy than the vapr, like the 2 ones lighter than it from BMW and also from MLD themselves. obviously less durability, but its probably not as marked a difference as you'd think, if something punctures through cuben would perhaps also have gone thru spinnaker in the same situation. To reduce the claustrophobia, I guess you could use a quilt and torso pad, or just chill on top of the bivy : ).

For me, it would depend on the weather. If it's humid, like most of the weather in my neck of the woods tends to be, I'd probably go with option 2, especially having no experience with the BMX Vapr bivy. However, Option 1 looks like the over all best use of space for many of the weather conditions you'll likely encounter.

However, my experience is extremely limited, so take it with a grain of salt :)

Tom