This is really good advice. One way of looking at custom basses is that you become the designer... So that means you better know ergonomics, electronics, tone and playability...
Which you might, if you're experienced with many basses, or a professional and have specific needs. But, if you're not, then there's scope for a sub-optimal design or combination of features which fail to live up to your expectations.
So makers like Bernie Goodfellow who offer custom options on a reliable template know what they're doing - with every combination a winner, hopefully suiting your needs. Jon Shuker has more diversity and options so when it works that's great, but there's more scope for creating an idiosyncratic bat-mobile of a bass.
My recommendation is to find a great bass you like from a maker and adjust the features to meet your needs, checking with the maker that it wont crapify your bass.