Interesting...Is this a splined coupler or a slip yoke? If a splined coupler, even if you did not separate the spline section, you might have an issue with spreading or thinning the OE grease by extending the coupler and returning it to the normal/operating position. Please clarify whether this is a splined coupler or slip yoke. If migrating grease was an issue, it sounds like a slip yoke...
On aftermarket shafts with splined couplers, a special "coating" on the splines often acts as a friction barrier. This is typically blue in color, and you've seen it on custom drivelines with splined couplers. As for slip yokes, a spline matchup with the original position is seldom considered, and unless you carefully mark the slip yoke and transfer case output splines, there's very little likelihood that the shaft will end up at the original spline alignment. Repositioning the slip yoke on the transfer case output splines would seldom create an issue unless there is abnormal spline wear on either the coupler or the output.
Of course, with a splined slip coupler, you must have the driveline's U-joints aligned or "in phase". When a splined slip coupler is taken apart and reassembled, the U-joint and flange position at each end of the driveline must match and be in alignment. Additionally, with a balanced driveline, these matched positions must also be consistent with the position of each U-joint flange when the shaft was built and balanced.