Choosing a preamplifier - synergy vs. matching components

I’d put the amp in your system first, let it burn in for a couple hundred hours, and then see what you think.  If the amp, say, adds just enough warmth then adding their pre may be too much of a good thing.  Wait to see how it sounds and then see what direction sonically you wanna go with the preamp.  I’d always side with a separate phono pre — it’s too important, and rarely will the phono pre in a preamp compare to a good separate unit.  FWIW, and best of luck. 

Should system synergy be the priority, or can better sound be achieved by carefully selecting and matching individual components?

There is no universal truth.  Sometimes there is a significant synergy between preamp and amp like Audio Research, but non-matching brand success can be achieved with other brands.

Is it preferable to choose an integrated preamp with a phono stage, or is it better to go with separate components?

Integrated components save money in casework and cabling. It’s less flexible for future upgrades as both the preamp and phono must be changed together.  The sonic quality of the built in phono is also important.

Separate components cost more in casework and cabling, but is expected to perform better as external phono stages typically perform better than internal phono offerings.

How does a SUT (Step-Up Transformer) factor into this?

It changes the sonic profile usually subjectively for the better.  The OPs Denon 103R and at least the stone Koetsu are known to sonically benefit from SUTs which must be used with “voltage” phono stages.  Obviously a SUT is an additional expense, and SUT using silver can be pricey

Alright.

I see that there are positive sides to both directions, but perhaps I'm too much of a beginner to start matching components without having an idea what results it will bring beforehand. 

I'm corresponding with a gentleman who recommended me to look at Abbas Audio and his philosophy and approach to high fidelity is that of Sakuma and Shindo-san (that probably also makes it appeal to Yamamoto Sound Craft). 

Sticking with Yamamoto Sound Craft CA-04 is the convenient and obvious solution, but I was trying to see if I could gain some advantages by investing in another product that could compliment the VT-52 amplifier with greater and even better sound. 

Should system synergy be the priority, or can better sound be achieved by carefully selecting and matching individual components? 

Both clauses question the process for reaching the same end - system synergy - the first by brand maintaining integrity the second by mixing brands.  If you like the sound of the brand, then maintain brand integrity recognizing that both positive and negative attributes of the sound will be reinforced.  Maintaining brand integrity will not present issues with electrical compatibility as a plus.  If you like the brand sound but feel there is an attribute to the sound you wish to improve upon, the best route to synergy is mixing brands that perform better at that attribute.  When mixing brands, verify electrical compatibility.  For example, is the preamp voltage output adequate to drive the amp?; is impedance a match?   Modern amps and preamps have less of an issue with electrical compatibility, but just assure they match or ask your dealer.  I have successfully followed both paths.  Most important, do not overthink it and use your listening skills to make the decision.  

@apollinaire ..I was trying to see if I could gain some advantages by investing in another product that could compliment the VT-52 amplifier with greater and even better sound.

Is this about the best functional result, or reduced cost - trying to intermix brands...

What logic or parameters are you considering, arriving at these conclusions?