LTNman
A quick check on the Citalia website shows that using LGW as the baseline, SEN departures are about 5% more expensive and LCY about 20% more expensive. I would think that those figures make SEN quite an attractive proposition taking everything else into account.
I do agree with you that the current lack of early morning train arrivals at SEN from London is a problem and I know every effort is being made to resolve the situation. As far as getting to/from SEN by road is concerned I don't see there is any problem with SEN being designated a London airport, especially as both the A127 and A13 can be used in the event of delays on one or the other.