Don't use pixel art resizers. They change the graphics and sometimes ruin things with their wrong assumptions. You could make it optional i suppose. But if you want to use your Amiga for actually making graphics it would really get annoying.
btw there is no such thing as 288p mode in Amiga - it can be 312p or 313p mode
Well technically maybe, but not all lines are visible, only 576 of the 625 lines are "active" according to the PAL standard. (some of these Inactive lines occur during the vertical blank, and were used to encode teletext signals)