This doesn't seem too complicated to work out how much you should expect to pay. I did a few checks to see how much the YQ is on EI using Avios. As you rightly mentioned it is not possible for BA to calculate the taxes for your itinerary commencing from either CUN or MEX through to DUB via MIA on AA and EI.
BA is quoting £51 for taxes and fees CUN‐MIA on AA. No YQ. For MEX‐MIA on AA it is £73. No YQ. The Int'l Airport Departure tax (Mexico, XD) is £50.40, almost double that of Cancun.
For MIA‐DUB nonstop on EI, the total amount will include US airport taxes and fees of exactly £25.50 and YQ of £74.50. See below:

I would be expecting to pay the total sums of each separate Avios itinerary so for your new itinerary departing MEX it would be £73 + £25.50 + £74.50 (YQ) = £173. BA is definitely quoting YQ for the EI flight and it looks like you initially paid it on your original itinerary.
Your ITA matrix calculation is incorrect as you have indicated BA for your itinerary. The £70.40XO (Mexico Transportation Tax) as well as several other lower quantity tax components are not applicable to your itinerary.
Originally Posted by
JWCurtin
For context the current calcualtion on ITA Matrix for our new proposed flights is as follows: MEX BA X/MIA BA DUB Q14.00 M 1948.00Y1N0C9S1 NUC 1962.00 END ROE 1.00 XT 8.60S1 50.40XD 70.40XO 5.50YC 5.50XY 3.00XA 4.40AY 209.40YQ 3.60XF MIA4.50