I would be surprised if that were the case. As far as I can see, from Colton Junction there are four tracks being newly electrictrifed to Leeds/Normanton and there are four tracks already electrified towards York. It would be odd not to tie together all four tracks at the same time.
At the junction itself, where there are six tracks side-by-side, Google satellite view shows the shadows of electrification posts on all six tracks.
All 4 tracks from Colton Junction to York have been electrified since the ECML upgrade in the late 80s/early 90s. This included an overrun length onto all 4 tracks towards Leeds.
The project has indeed electrified all 4 tracks between Church Fenton East junction and Colton Junction, so they will, at some point, be tying in all 4 tracks.
However, it is possible that they decide to do the tying in in two stages, with the Leeds lines closed but York-Doncaster available for 1 weekend, and the Leeds lines open but the York-Doncaster line closed the other weekend. If this is the plan, I wouldn't want to also close the north end of York station because managing the passenger load isn't going to be easy either way.