It is mainly because of the heavy push-rods and long stroke (86 to 90mm) of the RE engine. At low RPMs, the RE engine takes almost half a second to complete one stroke, making the exhaust stage last much longer than usual. The fuel-air mixture that explodes during combustion stroke increases the pressure inside the cylinder much higher than a 150cc engine. So during exhaust when the exhaust valve opens, the gases rush out in an explosive blast, producing the thump.
The reason it has a large pushrod and long stroke is because the engine displacement for this bike is 350 cc in a lean-burn single cylinder. Very few bike makers across the world use a single cylinder for an engine displacement as big as 350cc or even 500cc. This is because such an engine develops a slow revving or thumping characteristic which is contrary to what one would typically find in sport bikes, which in one twist of the throttle vrooms up to 10-12,000 rpm while if you twist the throttle of a Royal Enfield you will realize it will thump its way to max 4-5000 RPM. Long-stroke engines produce high torque at low RPM but less power at max rpm. Short-stroke engines produce low torque at low RPM but more power at max rpm.