Going into lecture mode:
If you look at period illustrations you will see that the "shot" was arrayed in multi-rank sleeves and bastions around the pike blocks. These would in fact be "lines" not skirmishers, IMO. They did not leave the immediate protection of the pike formation. Skirmishers would of course be dispatched from the main formation.
Unfortunately the scale of this game (grand-tactical) does not allow for a detailed representation of all the formation shapes, types, and gyrations they went cycled through. In the time frame depicted the shot could deploy, fire and recover to protected positions behind or inside the pike block. Therefore , shot and pike deployed in the same hex should be both fully fire capable and ready to receive a charge at the same time - at this game scale. That is, it would probably be more realistic to have unit types which have both shock and fire capability to take into account what was possible in 10-15 minutes.
Furthermore, position in a hex should have nothing to do with whether shot can fire, because the men moved forward and back in file, not rank. The first rank would fire and they move to the back of the file and start reloading. Each rank would do the same. More ranks meant more firing, not less. The number of ranks was determined by the amount of shot available and the formation width they needed to cover.
17th Century (30 Years War) actually much more flexible and closer to 18th century formations, when both the Dutch and Swedes first began utilizing pure musket formations not unlike those in the 1700's, albeit with more ranks because of slow reload times.
IIRC volley fire (depicted in the first fire bonus) was not "invented" during the period of REN. Heck, even marching in step was pretty much unknown.
Back on point. Formations were of course cumbersome and large, so having different units entering a hex cause disruption is accurate. However, pike and shot should not have this effect on each other - at least for movement purposes. It is also worth noting that these formations were not just a mish-mash of men armed with different weapons, but were formations which trained and fought together as "companies" or "regiments" under the banner of their "leader".