All dialogs are centered by the window manager (matchbox in this case), I think.
Disabling the busy dialog should be fairly easy though. Check out sysd/busy.c which has a "dialog_delay" after which the dialog is shown (default is 1 second). Increase this time or remove/disable the timeout completely.
The flashing LED is controlled from sys_update_rgb_led() in sysd/system.c.
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