In the new 7.x version of the MTP Add-on's for NT7 (as well as in the NT8 version), all of the main settings are now saved with the indicator settings and will be restored when you relaunch the application - Entry Order Mode, the settings for Auto Trade Management options (but not whether they are enabled, which is intended to be explicit), etc. "Override position size" is also intended to be selected explicitly since the intention of the software is to calculate the position size, though it would not be hard to enable the setting to persist.
In the NT7 version at least, the background of the trade module panel does change based on whether you have selected a Sim or Live account, but it is not configurable at the moment. Instead, it uses the same colors as the Default chart trader colors in Ninja. However, making this configurable is doable. In NinjaTrader 8 it's a little tougher because it's written (mostly) in WPF and they are using styles and themes to control the styling, which the product is inheriting to ensure a consistent look and feel with the main application.
Also, at the moment, the trading account is not persisted because the account is associated with a connection and there is no guarantee that the account will be available at any given time, and definitely isn't until you at least connect to the appropriate connection. However, this is on the enhancement list and may be possible as long as there is a graceful fallback mechanism in case the previously selected account is not available - for example, switching from a real broker connection containing a live account to just an IQFeed, eSignal, or a Market Replay connection, all of which contain may different accounts or not contain the original. In other words, it isn't quite as simple as it sounds.
With regard to ChartTrader, there is an old "Position Size in CT" indicator property which will set it to the initial position size generated by the trade setup analysis. However, it is not subsequently updated as changes are made to the position size in the trade module. It was mainly done prior to there being a trade module. If there's enough interest, it would technically be possible to keep the position size in sync if changed, but beyond that, chart trader is so limited, there isn't much more you'd need to do with it at trade initiation time.