Could you clarify what you mean by 'encourage players to focus more strategically in their ship building' ?
Building multiple ships in a bounty hunter playthrough is more viable then running around in a single ship because the AI does not handle target-prioritization well. And by your own admission under your newly proposed paradigm, a 'One ship fleet' would still be viable.
If the goal of this is to prevent the complete-reliability on 4x4 reactors, I'm not sure replacing it with a complete reliability on even larger reactors is necessarily better. Furthermore, due to power transmission issues, reactors that output more power than a large reactor find it difficult to actually use all that power. Though increased battery size could mitigate this to an extent, before being limited by maximum crewmate speed.
And even then I don't think this will stop the use of large reactors so much as bring in the use of large reactors and the required mass reactor.
I think if an arbitrary mass limit was to be implemented, it should be through the FTL system. Limit FTL drives to one per ship due to interference and make them mass limited instead of just having a fall off range for area covered. This will give the same mass limit as the mass-reactor, but ties it to an in-game concept and could repurpose the FTL coverage bar to explain the mechanic.
Alternatively, and I believe this suggestion or variations of it has been brought up before, ship size could be limited by the control room, with larger control rooms giving more mass-limit, or limiting maximum crew via control room and letting that indirectly limit ship size.
If I remember correctly, ship size will be limited in the upcoming version by drydock size, with bigger ships not being able to fit. I suppose mass-limiting ships gives more freedom of form then ships limited to a grid in that a grid-limited ship will expand to fill the grid while a mass-limited ship may be any form it pleases.
I do not think a 40x40 block should exist, and that the hypothetical mass limiting part should instead cap at around 6x6 or 8x8 for the current maximum building grid size equivalent. Here's a 40x40 cube, (Goliath for reference).

Having a part of such grand stature would curtail ship designs by requiring them to fit in a 40x40 block. For reference, the maximum grid building size is 100x100.
P.S. To write in a screenshot, open it in an image manipulation program such as GIMP or MSPaint and use the text tool, or do it by hand.
P.P.S. In game reactor sizes are 2x2, 3x3, and 4x4. There are no 5x5 or 6x6 reactors in the unmodded game. There is no 6x6 block in the unmodded game.