The Scotch Yoke mechanism provides a harmonic, or pure sinusoidal, piston motion. The scotch yoke was (and still is) the weak point of this design.
The longer dwell of the piston near TDC is the strong point for the Bourke engine: the fuel or mixture finds better conditions into the combustion chamber, during combustion. Bourke engine can operate with high compression, lean mixture and self ignition (based on the active radicals from the previous cycle). A technology lately re-invented, HCCI .

Compared to the Bourke engine, the Pattakon PRE engine provides even longer dwell near TDC. Roughly speaking: if Bourke's engine increases, compared to conventional, the dwell of the piston near TDC for x%, the Pattakon PRE engine increases, also compared to conventional, the dwell of the piston near TDC for 2*x% (i.e. twice as much as Bourke engine does). See the relevant plot at Pre-TDC (the green curve or Harmonic stands for Bourke's piston motion profile).

Pattakon PRE engine uses the conventional crank-rod-piston mechanism.
The 30 to 40% of additional time near TDC makes the Pattakon PRE engine capable to operate efficiently as compression ignition (Diesel) in some 30 to 40% higher revs than conventional Diesel engines (look at the Droplet animation). This way the naturally aspirated PRE Diesel competes the power concentration of the naturally aspirated spark ignition engine.   

In the Junkers-PRE arrangement the engine uses two short stroke pistons to form a long stroke combustion cylinder. For instance, a piston stroke of 50 mm gives a 50+50=100mm deep cylinder. Respectively, the mean piston speed of the 100mm piston stroke conventional is twice the mean piston speed of the Junkers. The same is the fact for the piston acceleration. In tanker engines (like Sulzer, Mitsubishi etc) the mean piston speed defines the reliability and efficiency point (for similar cylinders and same revs, Junkers-PRE operates at half the mean piston speed).
For the same "piston stroke" Bourke engine and Junkers-PRE have similar overall length (to compare the two arrangements open the PRE14.exe and Bourke.exe animations on the top and the bottom of the screen). During combustion, the surface of the walls around the combustion chamber is twice as much in the case of Bourke engine compared to the Junkers-PRE (the two cylinder heads of Bourke have been eliminated).
The lubrication of the Junkers-PRE is, in fact, a four stroke lubrication (the oil rings of the pistons never pass over the ports). Wankel engine cannot help consuming oil, Junkers-PRE consumes no more oil than the state-of-the-art four stroke.
The presence of two crankshafts initially appears as a disadvantage. It is not. A new level of balance for the internal combustion engine is achievable. The two opposite pistons absolutely balance each other. In case of equally distributed load on both crankshafts, the Junkers-PRE transfers neither inertia nor combustion vibrations to the basis. For instance, a Junkers-PRE having an electric generator on each crankshaft is an absolutely balanced power plant, in terms of inertia and combustion vibrations to the basis (ideal for Hybrid cars, autonomous robots etc).