Hello Sebastien,
"one Q-notification by inspection lot" applies to Inspection lot only irrespective of Notification type and it will set other notifications in-process if you record new defects.
In your case i guess both A1 and B1 are customized notification types. And in B1 notification you have incorporated "inspection lot" field by using some Exit.
When you create manual notification B1 using QM01, you enter Inspection lot number and it hits Table QMEL. Now when you record defects and create notification A1 system gets another Notification with the same inspection lot number and puts it In-Process.
Now if you consider standard notification types F2, Q2; When you go for QM01, you can not maintain Inspection lot number in Q2 notification, but for F2 (Automatically) system copies inspection lot number into notification. And as it does not get any other entry in QMEL there is no effect on F2 notification created earlier.
Experiment on user Exit QQMA0030 Check validity of status change; and see if you can restrict putting notification in-process if Notification type is Not Same.
Amol.