Good thinking - it shouldn't make a difference (as it is the same AY aircraft) but apparently it does (I guess different airlines will have a different view of the risk for misconnections that they are prepared to take).

So if it is a BA codeshare that means flight BA6005 - and the odd thing is that indeed ITAmatrix will not allow a connection from BA6005 to AA1587 (the 16:10 flight to PHX) - but as far as I understand it, the connection is allowed in the MCT exceptions list.

Results from https://www.ExpertFlyer.comMinimum Connect Times:
Connecting at JFK
Incoming airline BA
Outgoing airline AA

STANDARD.D/D...D/I...I/D...I/I.
ONLINE 1.00 1.15 1.45 2.00
OFFLINE 1.00 1.15 1.45 2.00
** OR * ARE ALL
BA-AA DD .45 FLT 1500 - 1640 - ALL DUB - ALL
BA-AA DD .35 TRM 8 - 8 CANADA - ALL
BA-AA DI .45 FLT 1500 - 1640 - ALL DUB - ALL
BA-AA DI SUP CANADA - CANADA
BA-AA DI .40 TRM 8 - 8 CANADA - ALL
BA-AA DI 2.00
**-AA DI 2.00 ALL - FLT 8880 - 8969
**-AA DI SUP CANADA - CANADA
BA-AA ID SUP FLT 1500 - 1640 - FLT 7295 - 7437 ALL - LAX
BA-AA ID 1.15 FLT 1500 - 1640 - FLT 1 - 6099
BA-AA ID 2.00 ALL - FLT 1 - 6099
BA-AA ID 1.15 FLT 6000 - 6099 - ALL
**-AA ID SUP ALL - FLT 1 - 9099 CUBA - ALL
**-AA ID 2.00 TRM 7 - 8
BA-** ID 1.45 FLT 4200 - 4299 - ALL
BA-AA II 1.15 FLT 1500 - 1640 - FLT 1 - 6099
BA-AA II SUP CANADA - CANADA
BA-AA II SUP MEXICO - MEXICO
**-AA II SUP ALL - FLT 1 - 9099 CUBA - ALL
**-AA II SUP CANADA - CANADA
**-AA II SUP MEXICO - MEXICO
BA-** II 2.00 FLT 4200 - 4299 - ALL

My understanding of the line I have highlighted in bold is that connection from any flight with number BA6000 to BA6099 to any AA flight has a MCT of 75 minutes. Maybe though there is a rule regarding precedence to exceptions higher up in the list? (e.g the line above that I read as "all BA flight numbers to AA flights from AA1 to AA6099 have a MCT of 120 minutes").