Hello, dear!
I can see clearly you did your research and thinking, and you did it well and thoroughly. Also, the smart choice of a rather more expensive stroller/stroller system that will actually last you and serve you well (and not saving money on this everyday used thing that is working best if it's high-quality and functional) is also admirable. I must say I like the three of your choices, and I will go through them with you here.
Firstly, the Bugaboo Fox 2. It is a great stroller because of multiple factors, the first of which is usability also there because of the low weight. It is very good to maneuver, even if on uneven terrain, and it is beautiful, high-quality, and functional. A thing to consider is still the low weight, which is a great thing and also makes it easy to load/unload it from the car, and the overall push experience is made better because of that... BUT, it also makes it so much less all-terrain then its predecessor, the Bugaboo Buffalo. I WOULD buy it for normal and some uneven terrain, also because it will sell so well even after getting the most of it... But for regular forest trails and a lot of terrain and dog-related adventures, I must say I see better possibilities. Still, I will end this part with 'You will not make a big mistake getting it', it's a very good, very nice stroller, very good to own and use. One last thing - even if higher-positioned, it's not that high, and this I would not take as the main factor (and the carrycot part is actually rather low-ish). It's all absolutely doable even for a taller person, but you should know it's nothing extremely tall - for a tall, all-terrain stroller, I would rather suggest a Stokke Trailz (a beautifully tall, even if robust model) or the older Buffalo, if you would even consider a pre-owned stroller system.
The Bumbleride Era is actually a much much better choice, all-terrain use-wise. The brand itself is high-quality and design with terrain use in mind (for many years already), so they do know what they're doing. I would take this one, even if maybe less beautiful and more functional. That also takes me to the reversible seat unit - as a first-time mom, you will appreciate so so much that after carrycot (if you are even planning to get that - I actually recommend getting it) you will be able to see your baby - around 6 months of age, it will be still so small, you will see. It is absolutely doable even without a reversible seat, but the transition time is harder, mainly if it's your first... It is better to see on your few-months-old baby for sure. So, the Era sounds the best from my point of view. And yes, it is lower, but I am also a taller mom and never had a problem with a lower model. It's not right on the ground, and also, it is you who will be pushing your baby mostly - the dad, not even giving birth, will be ok with a little bend to pick the baby up. The handle will adjust as he needs it, and even a rotating one, the Era is made well in the way that he should not kick the rear axle.
The Bumbleride Indie is, therefore, a very good model thanks to the three-wheels, this is true. The maneuverability is truly so nice thanks to the large front wheel... but, the BUT is the non-reversible seat, that is questionable from the side of if you will be comfortable with that little baby. And the Era, being a so much newer model, is anyway very good in those aspects that this model is so good to own, so I would say no need to push it. If I would be considering something three-wheeled in this case, I would actually rather look at a Mountain Buggy Terrain V3. With the carrycot option, you can actually use it in a 'reversed-seat' configuration after the lay-flat carrycot, because the carrycot is transformable to a reversible seat for those little babies around a half year. And it is a lightweight-enough model for such a capable three-wheeler.