By the way there is third option on Question 1. You can trade not martingale, but variable position sizing and again to have negative total pips and positive PnL. On Question 2 it is obvious of course, but often the cost is absolutely the same and even worse, because most often commission based brokers offer variable spread, which start at 0 pips but most often rise up to 1 pips on EUR/USD for example, than if you have 1$ per lot turnover fee, it is like having 1 pips spread plus the raw spread which is something like 0.4 so 1.4 spread, instead you can trade fixed spread 1.2 and it will be better.
No. With a 1000 Euro account and 1:100 leverage the max position you can open is 100,000 Euro. 1 Lot is 100,000 units of Euro BUT as commission is $5.5 per lot this will reduce your account to just below 1000 Euro so you will not be able to open 1 Lot in practice.