I disagree on this one - I don't see a major problem with General Bonaparte leaving the army in Egypt, circumstances were peculiar and he made a judgement call. Under the directory there were quite a few generals doing things on their own initiative (whether taking "cures" or suddenly having bad health at convenient moments) and Bonaparte in Egypt isn't in a position to check with Paris, which actually makes his action more justifiable, IMO. Risky, because he can't be entirely certain of approval, but justifiable. The Emperor Napoleon would have had a general doing such a thing cashiered, but those were different times.
But I also believe that Ferdinand was not simply running AWAY from Ulm but running TO Bohemia to continue prosecuting the war against France (after Mack had decided to give it up). The quote that Elting provides about denying the French the honor of capturing an archduke is not sourced (although it's in quotation marks) and until someone turns up a source for this I have to regard it as someone's opinion, and probably not Ferdinand's - and who but Ferdinand or someone he confided in would know his motivation with any certainty? It sounds to me like it's either from a French source (and thus propaganda) or from Mack in the context of justifying his own actions and casting blame on Ferdinand - either way from a hostile source - but that's just my conjecture. There is a possibility that I'm misjudging Ferdinand by looking at what I know of his actions and he actually said something like this, I suppose, and if the source for Elting's quote turns up we can see if this is the case. But it seems that Ferdinand considered his presence in Bohemia essential or at least beneficial to raising a new corps to fight the enemy (perhaps with justification), even if nothing more than as a rallying point. How different from Napoleon considering his presence in paris in 1812 to be essential in raising a new army to continue fighting the enemy? perhaps indicating that Ferdinand had an overinflated sense of his own importance, but important to consider in weighing motivation, especially in the context of having his command subverted by his chief of staff on secret orders from Francis.