I'll answer your questions based on your/my numbers.

1. So, if I change my equipment profile or system set up in the master recipe, what happens to all the previous batches which are archived?
--They reflect the original profile you brewed them with. If for some reason you delete or edit that original equipment profile, the previous batches using that profile simply say "Specific to this recipe" for the equipment profile.
1. Continued...I brew across many different systems: 3 l BIAB, 10 l BIAB, 16 l both BIAB and mash tun, 20 l mash tun and it would seem to me that if I scaled the recipe to the particular system I plan to use for that session, I don't want to have that change reflected in the past archive batches.
--It wouldn't be. You have a master recipe and the batch. In both you can mess around and change it however you want with profiles, hopping rates, gravities, water volumes, efficiencies, etc. None of that is ever changed anywhere except the batch or recipe you are currently working on. Any changes to the original recipe are reflected in any batches you create after that based on that recipe though.
2. Is there an option not to update the copies of that recipe in other folders? If I have copies of recipes in different folders, they are separated for a reason.
--Yes...this would function like BeerSmith. You would actually make a copy of the recipe. When you do this BeerAlchemy adds -copy to the end of the recipe name. Then you can go in a change it to whatever you would like to call it. So let's say you have a recipe for a Vienna Lager that you want to share. Before editing it to get it ready to share with a friend, you simply create a copy of the recipe and make whatever changes you want to the recipe and then export it as BeerXML and it's good to go.
2. Continued...I do not want this change to be reflected in other copies of that recipe. I also use the 'brew log' folder to plan brews for the upcoming season and will tweak recipes in that folder for the upcoming brew. I only want that particular copy changed, as I don't know if the change will be one that accomplished my goal for that change.
--This is what the "Batches" are for. You mess with the batches while keeping your original recipe the same. If you brew a batch and you nailed it and want that to be the "Recipe" going forward...there is an option to "Promote Batch" which means it's no longer a "Batch" it's a new master recipe. Super simple with a shortcut even.
4. As I mentioned above, I plan out my brews. I can see this being of value to someone who is less OCD than I am. At the same time, I always keep a good inventory of my most used malts and hops along with at least 2 to 4 strains of yeast being propagated, that I can change my brewing plans at the last minute and still make most of everything in my 160+ recipes (actually, I lost count waay back) in BeerSmith.
--I plan my brewing calendar a year ahead too.

I've never actually used this feature which is why I said that points 1-3 are the main reasons. I know some people like this feature though so I mentioned it.
5. If you are interested in looks, I am glad you found BeerAlchemy. The UI is a constant complaint from those who are looking for a well polished program. While rounded buttons and flashy colors are great, they really don't impact the usability of a program. This may have been one of the main reasons I stopped programming computers in the mid 80's.
--Yep. Mac programs are used by Mac users.

And I know how this bunch can be. It's not a big deal to me. Just something that is pretty blatant.
All-on-all, I wish I could get Beer Alchemy for my PC to throw it around the streets for a bit and see what features are really good and where the potholes are.
--If you have an iPhone or iPad it's available for both.
Cheers!