This is exactly what I did with my DD (2nd child) & it didn't cause any problems. In fact we did all naps in the sling until she was 2mo, then started 2 out of 4 in the cot.
I just tried to be consistent. I did first and lunchtime nap in cot as I guessed these were ones she was likely to keep the longest. She would sleep 2-3 hrs in the sling but only 30-40 mins in the cot, regardless of A time, swaddle, routine, dark, white noise etc.
I would alternate cot and sling naps so she had some long ones to avoid OT, so we could leave the house with her older brother and to give me a break, but also cot ones meant she was still learning those skills.
As she got older (closer to 4 or 5mo) she switched to only taking short sling naps but longer cot naps, so I was able to just go with cot naps