As no. 1 piston is on the intake stroke the cylinder is filling with the intake charge. Due to the crankshaft design of 120 degrees between throws the ajoining cyl, no.2 intake vale breaks off its seat and the no.1 cyl stops filling.
The adjacent pairs are as separated as they can be.
The center #3-4 pair have symmetrical 360° - 360° - 360° interval of separation.
The #1-2 and #5-6 pairs have an irregular interval: 240° - 480° - 240°, etc.
If the intake duration exceeds 240°, the later cylinder will cause a minor leak as its valve begins to open, but since this is BTDC vacuum is minimal, and no actual flow will occur until the piston moves down ATDC a bit and the lift reach perhaps .020". The earlier cylinder is already coming up to compression in any case.
In addition, #1 & 6 do not have this problem, since their complementary cylinders (#2 & 5) are 480° later and cannot interfere.
Swapping the lobes to substitute 2 for 5 will subject the crank to higher torsional loads. Development of L6 engine blocks and cranks dates to before WW1; everything you can think of has been tried, patented, and in most cases failed. I can't find an L6 with a firing order that places 3 power strokes at one end of the crank, then 3 at the other.
Dividing the ports will certainly cure the EFI distribution problem, but will reduce peak power as all the racing head prep has show. There's just not enough port area.
