Modification of an alignment while doing pairwise alignment

Pairwise alignment of two sequences may be a time-consuming task. Currently different features that may affect the data are enabled while the pairwise alignment is in progress. What if an alignment is modified at this time?

Scenario:

1. Open at least two sequences in the Alignment Editor that are long enough (for example, use chromosome Y of human and macaca mulatta), i.e. export one of the sequences to an alignment format and add the second sequence to the alignment.
2. Open the "Pairwise Alignment" tab on the options panel.
3. Set the sequences (the first one and the second one).
4. In the "Output settings" group uncheck "In new window".
5. Click "Align".
   Expected result: features such as "Align" are disabled until the end of the pairwise alignment task.
   Current result: the feature are enabled.