Looking at the modern iterations of the program guidelines for these programs, especially [1] and [2], you basically have to use the flag, the text over, under or to either side of the flag (your choice) in one of 6 fonts (Arial, Auto, Calibri, Garamond, Tahoma, Trebuchet, Ubuntu or Verdana), and have some rules for minimum distance, minimum size and proportionality. They absolutely could have made those two match visually. But each program offers premade banners that match the design criteria, and those don't always harmonize. As you say, nobody cared

1: https://hadea.ec.europa.eu/programmes/connecting-europe-faci...

2: https://commission.europa.eu/document/download/3192a0ef-6bda...

3: https://ec.europa.eu/regional_policy/information-sources/log...