I see no contradiction.
A Traveller, or I assume sophonts in general, can only use Expert software as a replacement for INT and EDU skills.Core, p106, Expert:
Expert software packages mimic skills. A Traveller using Expert may make a skill check as if he had the skill at the software’s Bandwidth -1. Only INT and EDU-based checks can be attempted. If a Traveller already has the skill, then Expert grants DM+1 to his check.
The same is not true for Intellect software or robots, see CSC p68 and p71 (Astro-Mech Droid with Pilot skill but no hands).
This is completely consistent with Core, p155, as far as I can see:CSC, p68, Intellect:
An Intellect software package is similar to the more primitive Agent but has a far more advanced intelligence, being able to communicate normally with a Traveller. It is capable of using any Expert package and can simultaneously use a number of Expert packages equal to its Bandwidth.
Core, p155, Automated Duties:
A ship running an Intellect program and Expert Pilot can act as the pilot.
I do not consider that a house rule, but simply RAW. See e.g. Core, p107:
Note that this explicitly applies to weapons, hence in general DEX-tasks.Core, p107, Expert Skills:
Having a tool or weapon with the appropriate Skill Expert program and an Intelligent Interface can grant a Traveller DM+1 to his checks.
I see the statement about Expert software this way:
This is consistent with p107, in my opinion.Core, p106:
... A Traveller using Expert may make a skill check as if he had the skill at the software’s Bandwidth -1. Only INT and EDU-based checks can be attempted. [Line break added]
If a Traveller already has the skill, then Expert grants DM+1 to his check.
This interpretation makes all the rules about Expert software valid and consistent. Your interpretation seems to rely on that most of these rules are simply wrong.
I can agree that the rules are not intuitive or perfectly clear.