Series 1 engine anomalies

Have a series 1 with the original engine according to the Cumbrian archives.
First registered june 1959
The engine number starts 77...
It has the larger exhaust studs.
Later style crank and mag housing.
Groove for oil thrower washer.
If I didn't have a copy of the original registration entry I'd just have assumed someone replaced the engine with a later one.
Would it have been likely that these mods were made retrospectively or did innocenti make these changes earlier than is thought?
First registered june 1959
The engine number starts 77...
It has the larger exhaust studs.
Later style crank and mag housing.
Groove for oil thrower washer.
If I didn't have a copy of the original registration entry I'd just have assumed someone replaced the engine with a later one.
Would it have been likely that these mods were made retrospectively or did innocenti make these changes earlier than is thought?