Not the worst habit in the world. If you were doing all four wheels and the MC reservoir was anywhere near Max you could easily overflow the reservoir and would want the cap off and a large shop towel underneath in case you didn't catch it in time. Just leave the cap on and check the level before pushing back the next set of pistons.

Do take heed of Bruce's comment that the pads should not be tight in the slots -very common when replacing pads and quite likely your major problem. He normally hits the nail on the head with the first blow. I also imagine your pistons are pretty gummed up and your seals may be worn by now. Short of a rebuild with new seals, a good temporary solution may be to remove the dust covers, clean your pistons up with old brake fluid and a tooth brush, running the pistons in and out up against a pad backing plate a few times as you go until no more residue is pushed out, followed by a final go with brake cleaner to get rid of all brake fluid residue. You will likely be very pleased with the results so it is worth the effort, but it won't be a fun job out in the cold and wet. Not only does that aid braking by having all the pistons extend uniformly together, it also helps the pads to retract properly when released and keep them from scuffing on the rotors as well as extending the life of the seals. To keep brake squeal at bay, it's a good habit to apply a bit of high temp brake grease between the pads and shims and a glob between the piston end and the shim. Padded shims can help and people often use them instead of worrying about brake grease, but I personally prefer not to use them unless I'm trying to deal with bad squealing as they add to soft braking. Any scoring on the rotor will reduce braking, especially initially, making for a softer feel. I agree with Art's comments -new pads sometimes do need a bit of time to break in (no pun intended) and getting used to. You may want to hasten the bedding in of new pads with a few hard stops from higher speeds, especially if they're the harder ceramic pads.
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Dave -940's, prev 740/240/140/120 How time flies when you're having fun