Well, I haven't dealt specifically with any of that, mine is more starting a business, not running one, but whatever I have been doing, which is on small hydro plant and tea cottage factory, I have found online portals to submit my stuff, except for WRMA, and I guess for me, I normally call a friend who call a friend, and I send somebody to get me somewhere.
For me the ease of business is there. The cost of business is something else. That is why I realize to manufacture anything - I need to start from generating my own electricity. The biggest business risk is KRA sending you tax bill you can't pay. Labour I think is easy to sort - there is mismatch btw min pay and what people are willing to take...so you can play around that.
I can confirm none of those licences are payable online. You have to hustle them for weeks and months especially those requiring physical inspection.