In this case, it makes the entire system somewhat useless. We will be able to save heroes and continue playing with them, but there is not the slightest motivation to develop them or improve our relations with different NPC factions in order to get various mods and combine them on the heroes.
If instead of implementing a cool system from the campaign, we will be waiting for a modified window of a regular game - it will be a waste of a good idea.
Given that we are given the opportunity to almost unlimited combination of races/special technologies on the troops and factions, the possibility of full development of the hero (and transfer it between planets) here is the smallest problem for the balance, which is only possible. Many players, however, are very much looking forward to this feature, perhaps more than anything else in this new mode.
______________________________________________________________
Updated:
Since we are given complete freedom and the developers say that this mode is so unbalanced that it can not be done in multiplayer, it will be very strange if the only chip that caused rejection from the development team will be one of the coolest gameplay chips in the entire game - the progress transfer system (levels, items) just like in the campaign. Then you will get a Galactic Empire, where there will be no development of this very Empire - the ability to take new units with you is, of course, cool, but this is not a system of progress. In an extreme case it is possible to make a separate setting for menu settings/difficulty.
I hope that I am wrong about this and we will still see a complete transfer of the system from the campaign, otherwise my hype about the new mode will subside greatly. In theory, without a possible transfer of progress, I don't even really see the incentive and sense to play this mode compared to regular games.