Base on my experience, Yes, they are gonna re-dye it and the shoes are gonna be darker, you may interest in the restoration review that I wrote up http://stevefok316.weebly.com/home/alden-restoration-service-review
TSM and Supply & Advise have something similar to what you are looking for, but both with leather sole. http://www.theshoemart.com/alden-mens-9-eyelet-perforated-cap-toe-boot-shell-cordovan-color-8-d5812 http://www.supplyandadvise.com/products/perforated-cap-toe-boot-color-8-shell-cordovan-d5833h?variant=16506045572 If you are OK with straight tip, Alden DC has Straight tip boots with commando sole on grant last.
I think they are both versatile enough to pair with many outfits. In terms of comfortability, flannel will be better as some people find tweed a bit scratchy In terms of care and durability, tweed is better as its harder to get wrinkle and tweed usually get a better longevity than flannel. I personally prefer tweed.
Agree with others that the reverse welt is the better option here. Frankly speaking, I am glad that someone finally decided to make a shell Vtips with reverse welt. I have a suede Vtips with reverse welt and I think they look better than the flat welted Vtips. I think Brogue's shell Vtips will be a signature make-up, don't hesitate, jump on it!