On balance, I think it is better to have the bolts drop down from inside, if you can do it. As you say, there are a couple of AN3 nuts and bolt-tails in the way. During the build, if you can loosen those enough to drop the bolts in from the top, thats good.
If it turns out the bolt isn't long enough, because your Grove gear are thicker than standard steel gear struts, you will have to reverse the process to get those out and put longer ones in. So just be prepared for that possibility. (you may also want to switch to NAS6606 bolts, see below).
Pros: mainly that you will be able to torque the bolts by torquing the nuts on the bottom, which is a more accurate way to torque them. You will still need someone to put a wrench on the bolt heads inside the gear tower to do the torquing. The gear tower mod to make these more accessible is absolutely worth doing.(see note below)
Cons: Only really that the nut and bolt-tail sticking down will require a bigger bulge in the gear strut intersection fairing to cover them, compared to just a bolt head. Small price to pay if you ask me.
Most RV-8s have been built with the bolts installed per plans, up from the bottom, with the washer and nut inside the gear tower. This is OK, but it means that when you torque the bolts from below, with the torque wrench on the bolt head, you must add to the specified torque an additional torque equal to the friction torque to turn the bolt in its hole. Of course that torque changes as the bolt tightens because the slight deformation of the U-803 saddle makes the bolt rub on the side of the hole, so this is a less-than-perfect solution.
Finally, PLEASE PLEASE PLEASE be sure to use the strong NAS1804-6 nuts, not the horrible NAS679 nuts that are supplied with the kit.(or used to be, anyway). You may find that you need bolts with a longer threaded portion since these nuts have more grip length, so you would want NAS6606 rather than NAS6206.
The easiest way to be sure you have hardened washers is to buy them fresh. I think Vans has them, although I couldn't find them listed specifically in the 'store'. Or go buy SAE Grade 8 washers. With the NAS1804-6 nuts, there is not a lot of contact area on the base of the nut, so I recommend getting close-fitting washers (have a smaller hole in them that is a closer fit to the bolt). I actually think that getting more contact area under the nut from the tighter fitting washer is more important than the hardness. NAS1149 washers seem to have the closest fit specs (0.390" I.D.). A normal NAS1149-F-0663 (replaces the old standard AN960) is not very hard, but if you can specify NAS1149-G-0663, those are made of 4130 alloy steel, and are moderately hard. You may be able to order those from www.genhardware.com
(also a good source for longer NAS6606 bolts if you need them)
Note: I started with a Quickbuild fuselage, and the gear towers were all completed, so I didn't tackle the challenge of modifying them with the removable panel. In hindsight, I really wish I did. Doing that mod on the completed structure would not have been that hard, and it would have saved a lot of blood, sweat, swearing. I would definitely recommend doing it, even if it means back-pedaling on some other work, like final cabin parts installation, gear installation, panel, etc.