You should probably put a straight edge on the door and make sure theres no crazy highs or lows from the heat. The welding is pretty gnarly, you can do much better with a little practice and patience, but if you think you can fill it,without covering the entire door in filler go for it. Check the backside of the patches for rust too. Welding causes the area to flash rust almost immediately, so if they didn't treat those patches after they were done it'll be full of rust in there.....It looks to me like there's pitting on the bottom of the patches and maybe between the two. How are the seams inside the door(they're sometimes covered in seam sealer) and the area that the weatherstripping snaps into? Before you go fixing or filling, I'd look that door over inside out so I didn't waste my time. I figure if your worried about perfect panel gaps, these patches aren't up to what u want. There's a guy Corey Charlton in Northern Indiana. He might have a door for you. He's got a gbody junkyard. That's what I would do, or cut those patches out and try again. Especially if I'm right about the pitting.
PSA: I'm not a bodyman, I'm a construction worker so take what I say with a grain or 2. Research is key if you wanna be successful with this. I'm pretty sure Rktpwtd project oldscool thread has your name written all over it. D Explains his thought process really well, and gives insight into what's worth fixing and time Involved. I think he had a door dilemma on that car too.
Aside from that thread, Fitzees fabrication and Kevin tetz paintucation on youtube have been invaluable to me as I try to teach myself bodywork.