Hi Fabrice,
SpatiaLite and GPKG are two significantly different formats. They are
both based on SQLite but otherwise have very little in common.
SpatiaLite offers a basic support that allows you to read and write
a GPKG, which however remains an alien format.
if you want to use all the Spatial processing power supported by
SpatiaLite there is only one way to do it:
A) create a brand new SpatiaLite DB
B) import your data from GPKG into native SpatiaLite tables
C) do whatever you have to do
D) at the end of the work, if necessary, export all processed
data again to the GPKG
bye Sandro