First off... micrometers are only as accurate as the person using it.
Especially to 0.0001" accuracy. And dial indicators are only as accurate as the rack's machining.
I've been part of a test where a group of machinist's were given the same mic to measure the same object. Each took three readings.
To 0.0001" accuracy, none had the same reading, twice.
There was a 0.0008" spread between a few of the reading.
These were all very qualified machinists with many, many hours under their belts.
The chances of a ordinary, mechanically minded person, with limited micrometer experience, being able to repeatably measure down to 0.0001" is....well nonexistent.
OTOH, given a decent dial caliber, the same lay-person can repeatedly measure 0.001". And with a bit of instruction's can take that down to 0.0005" (half a thou).
Another note about precision measuring
equipment.
Calibration must be checked everyday if not before every use.
With a mic., this requires a standard to be measured then the instrument adjusted.
On a dial caliber, you simply close the caliber and adjust the dial to zero.
On to the OP's question, there is a time and a place for each instrument.
If you are measuring shaft dia., then either will do. I prefer to grab the calibers first because they are easier and faster. As long as "half a thou." is accurate enough. And if you have a "good" set.
For bores, such as cly., calibers are out of the question. For these you need a bore mic or telescopic gauge and a reg. mic..
If all you are wanting to measure is rocker shaft and arms, and if the caliber's ID reach is sufficient, then that is how I would go.
If you want to measure all
engine parts, then you really need to get a mic set and telescopic gauges.
But to be honest, if you are doing a complete reman., you are going to have the crank turned and block line bored and bored by a machine shop. Whom will tell you what bearings and rings to buy.