Should be fine. Don't forget that thermopiles, just like thermocouples measure the temperature difference between the target and themselves. That means if you want absolute temperature then you need a local absolute temperature sensor to determine the temperature of the thermopile itself, or have two thermopiles right next that are the same temperature (possibly by mounting them on the same block/pad of aluminum or copper) and have one point at a known temperature target. Or you could point at different targets to measure the temperature difference between two remote targets.
If all you're interested is in the temperature rise above ambient and the thermopile is far enough away from the peltiers to not be heated up, then you probably don't need to do any of this.
If all you're interested is in the temperature rise above ambient and the thermopile is far enough away from the peltiers to not be heated up, then you probably don't need to do any of this.