Nothing with regards to their product offering. Biggest mistake I ever made though was "upgrade" to their Private Client suite which is a bunch of bs. Most of the time you have to phone the relevant department anyway.
Bigger deposit can potentially mean better interest rate. If we put the interest rate aside, there should be no difference in repayments between having a R1 000 000 bond with R200 000 in an access facility vs a bond with R800 000 outstanding. The fundamental differences (and take it with a pinch of salt):
Access facility means just that, you have access to any extra funds you put in your account. Great for an emergency fund, but easy to spend if you are "bad" with money
Extra money in the access facility returns at the rate of your home loan interest but tax free. You pay tax on interest you gain but not on interest you save.
Down side obviously is that the rate of return is pretty low compared to what equities are returning, so having too much in the access facility is potentially bad given the low interest rates.
You cannot fix the interest rate on a bond with an access facility which is something people may want to do in a year or so's time
Personally - I took the access facility to keep my options and access to funds open.