Light and occasional knocking can be acceptable. All the time and heavy or medium knocking is not good and not acceptable. I have left using manual cars since 2010 and prefer automatic for many reasons; the automatic transmission has one of the great advantage that it usually does not allow knocking at least from driving parameters (not referring to bad fuel etc.).
Use of Hi-octane is usually a myth especially with regard to fuel economy. No doubt it will not knock (pre-mature explode in compression stoke) but one should go for good quality normal (Super) petrol. What is the guarantee that the petrol pump selling regular fuel of low quality would not sell low quality Hi-octane. Please note that Toyota 11th Gen (2NZ-FE, 1ZR-Fe and 2ZR-FE) are good for regular fuel with Reasrch Octane Number (RON) of 91 or higher. Avoid wasting money on Hi-octane and find a quality petrol pump BUT pay attention to your driving as you very rightly pointed out yourself.
I drove GLi manual 1.3 11th Gen 2015 of my cousin for brief 5 km only and came across knocking too. BUT I contribute this to my driving in which I inadvertently did gear shifting at much low RPM.
YES! You are 100% right in my opinion (keeping other factors aside) that you should REV up to higher rams before shifting. How much high rpm? Please experiment at various revs and find the most suitable ones.
PS: Knocking is produced because of pre-mature fuel burning/destabilising and should be avoided as it causes very high frequency vibrations of engine walls which if happening very often would result in damage!