Would joining pads of a pi-filter eliminate impedance changes from line to pad? Would it cause problems with alignment during reflow?
I can only answer the part of the reflow-soldering, I lack some knowledge about impedance.
Joining the pads that way will definitely cause problems during reflow soldering. The problem will be tomb-stoning. This is when a component is standing upright (feet up in the air) on the PCB during reflow soldering.
The components will float to the centre of the pad based on the force of the solder-paste.
For the horizontal component this will probably not be an issue because both pads are the same size so the force applied on both sides is the same (however too strong forces will result in tomb-stoning too).
For the two vertical components the side on the joined pads will float to the centre (the force is stronger on the larger pad than the force on the smaller one). Resulting in a shift and tombstone of the components.