You’d have to change the Neimodians holo transmission after the invasion force landed. It doesn’t make sense for them to search their ship for the Jedi, if they landed on Naboo directly.

However now that I saw this, I had an idea. What if we show how the Jedi pass the blockade, without the Neimodians taking notice? I’m imagining something like this:

-Crawl
-Sidious hologram
-Obi and Qui-Gon are briefed by pseudo 3PO
-Gunray contacts the Jedi’s ship, they’re asked to land onboard
-Wide Shot of the Jedi’s ship approaching the droid control ship, add in a tiny escape pod flying away
-we follow the pod and see the droid invasion fleet lowering to the surface
-from here on we’re back on track with the original plot

This would bridge the Jedi and the invasion plot and mirror the opening of ANH nicely.
All we would need is a model of an escape pod.