1. Don't allow businesses to customize at all, make them fit to you. That can work with something like ADP, but little else. A lot of the cool B2B startups think they can displace incumbents by just building cool, fast software, and then they are perplexed why they can't gain marketshare when every other customer has some bespoke use case they don't support.
2. Build a general uber-programmable platform that businesses can customize themselves -- now you are in the "slow", "poor user experience" territory but at least it works and is cheaper than option 3
3. Hire consultants to write bespoke products from scratch for each business. That's the old IBM Services model.
So if your baseline is Microsoft Office, then the performance/user experience of your favorite online B2B platform is going to be terrible. But if your baseline is IBM Services, then it's a godsend.