The customisation is good but its different than what we've seen in previous games.
Don't know if you played Mech 4 or MW5Mercs but each mech had energy, ballistic, missile hard points 99% certain that was for graphics but hey moving into Clans.
In Clans you have let's say 4 alternative configurations. While you play the game you/your Starmates earn XP oh that machine (the more you use it they better it gets idea). You spend that XP to unlock alternative configurations (which are really closer to TRO3050 configurations)
That's the first part of modifications. However there's more inside each configuration (which you can unlock in any order) you can completely strip that configuration and replace it with weapons of like comparison.
For example I have a Mad Dog (yes all Clan names are used for the original OmniMechs)
Standard Prime configuration has
2 large pulse lasers
2 medium pulse lasers
2 LRM20 with not enough ammo
I changed that to
2 ER Large lasers
2 ER Medium lasers
2 LRM15 with more ammo, heat sinks and armour
Like for like weapons within your configuration
I feel it works really well when you think about the OmniMechs - the Prime pod is designed to fire energy and ballistic weapons etc. I'm also pretty sure it's for a graphics perspective the machine expects a prime so missile and energy weapon graphics are used.
You can also tweak the performance of your Mech with your XP again the idea being a pilot has an affinity to a design so it performs a little better as you get used to it. So you can mod the top speed, acceleration, torso twist speed, torso angles etc.
You can also spend points from salvage on the researching improvements to all your Mecha equipment and weapons making them a little better as the game goes on (not canon but it's a game and it lets you see improvement as you go)